Are you using the same file i specify of Zelda for GBA ?
Filename : Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].gba
MD5 : 9edf4f6e19d901d470aa1117cb0372b3
CRC32 : 5a164321
For me the strange thing is yesterday with this specific game, the achievements works perfectly with retroarch 1.6.3.
After upgrade retroarch to 1.6.7 and mgba core, “this game doesn’t feature achievements.” i can’t understand it

Terminal output :
$ retroarch
[INFO] Environ SET_PIXEL_FORMAT: RGB565.
[INFO] Redirigiendo partida guardada a "/media/Compartido/Videojuegos/Partidas/Emulador/Bateria/.srm".
[INFO] Redirigiendo guardado rápido a "/media/Compartido/Videojuegos/Partidas/Emulador/Estado/.state".
[INFO] Version of libretro API: 1
[INFO] Compiled against API: 1
[INFO] [Audio]: Set audio input rate to: 29970.03 Hz.
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/16bits.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/8bits.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/inu.glslp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/pcsx_rearmed_libretro.so.glslp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/retroarch.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/retroarch.glslp"
[INFO] [Video]: Video @ 960x720
[INFO] [GL]: Found GL context: x
[INFO] [GL]: Detecting screen resolution 1024x768.
[INFO] [GLX]: X = 0, Y = 0, W = 960, H = 720.
[INFO] [GLX]: Found swap function: glXSwapIntervalEXT.
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [GL]: Vendor: NVIDIA Corporation, Renderer: GeForce 6200 TurboCache(TM)/PCIe/SSE2.
[INFO] [GL]: Version: 2.1.2 NVIDIA 304.135.
[INFO] [GL]: Using resolution 960x700
[INFO] [GL]: Default shader backend found: glsl.
[INFO] [Shader driver]: Using Cg shader backend.
[INFO] [CG]: Vertex profile: vp40
[INFO] [CG]: Fragment profile: fp40
[INFO] [CG]: Loading Cg meta-shader: /home/inukaze/.config/retroarch/shaders/retroarch.cgp
[INFO] Found #pragma parameter NTSC Intensity (intensity) 1.000000 0.000000 1.000000 0.050000
[INFO] [CG]: Loading Cg shader: "/media/Compartido/Inukaze/LinuxHome/.config/retroarch/shaders/shaders_cg/TV/gamma.cg".
[INFO] [CG]: Loading Cg shader: "/media/Compartido/Inukaze/LinuxHome/.config/retroarch/shaders/shaders_cg/misc/ntsc-colors.cg".
[INFO] [CG]: Found semantic "POSITION" in prog #1.
[INFO] [CG]: Found semantic "TEXCOORD" in prog #1.
[INFO] [CG]: Found semantic "POSITION" in prog #2.
[INFO] [CG]: Found semantic "COLOR" in prog #2.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #2.
[INFO] [CG]: Found semantic "POSITION" in prog #24.
[INFO] [CG]: Found semantic "COLOR" in prog #24.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #24.
[INFO] [CG]: Found semantic "POSITION" in prog #23.
[INFO] [CG]: Found semantic "COLOR" in prog #23.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #23.
[INFO] [CG]: Found semantic "POSITION" in prog #22.
[INFO] [CG]: Found semantic "COLOR" in prog #22.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #22.
[INFO] [GL]: Using 4 textures.
[INFO] [GL]: Loaded 2 program(s).
[INFO] [GL]: Using GL_RGB565 for texture uploads.
[INFO] [GL]: Creating FBO 0 @ 512x512
[INFO] [GL]: Creating FBO 1 @ 512x512
[INFO] [GL]: Creating feedback FBO 2 @ 512x512
[INFO] [udev]: Plugged pad: Microsoft X-Box 360 pad (1118:654) on port #0.
[INFO] [udev]: Pad #0 (/dev/input/event5) supports force feedback.
[INFO] [udev]: Pad #0 (/dev/input/event5) supports 16 force feedback effects.
[INFO] [Joypad]: Found joypad driver: "udev".
[INFO] [Autoconf]: 187 profiles found.
[INFO] [Font]: Using font rendering backend: freetype.
[INFO] [X11]: Suspending screensaver (X11, xdg-screensaver).
[INFO] [Autoconf]: selected configuration: /home/inukaze/.config/retroarch/autoconfig/udev/Microsoft_X-Box_360_pad.cfg
[INFO] [PulseAudio]: Requested 24576 bytes buffer, got 22272.
[INFO] [Menu]: Found menu display driver: "menu_display_gl".
[INFO] Found #pragma parameter NTSC Intensity (intensity) 1.000000 0.000000 1.000000 0.050000
[INFO] [Font]: Using font rendering backend: freetype.
[INFO] [Font]: Using font rendering backend: freetype.
[WARN] Input device ID 5 is unknown to this libretro implementation. Using RETRO_DEVICE_JOYPAD.
[INFO] No se guardará la SRAM.
[INFO] Found #pragma parameter NTSC Intensity (intensity) 1.000000 0.000000 1.000000 0.050000
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_favorites.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_music_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_video_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_image_history.lpl].
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Unpausing.
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Pausing.
[INFO] Using content: /media/Compartido/Videojuegos/Emuroms/Nintendo/G.b.a/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].gba.
[INFO] arg #0: retroarch
[INFO] arg #1: /media/Compartido/Videojuegos/Emuroms/Nintendo/G.b.a/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].gba
[INFO] arg #2: -s
[INFO] arg #3: /media/Compartido/Videojuegos/Partidas/Emulador/Bateria
[INFO] arg #4: -S
[INFO] arg #5: /media/Compartido/Videojuegos/Partidas/Emulador/Estado
[INFO] arg #6: -c
[INFO] arg #7: /home/inukaze/.config/retroarch/retroarch.cfg
[INFO] arg #8: -L
[INFO] arg #9: /usr/lib64/libretro/mgba_libretro.so
[INFO] arg #10: -v
[INFO] [CG]: Destroying programs.
[INFO] [CG]: Destroying context.
[INFO] [XINERAMA]: Xinerama version: 1.1.
[INFO] [XINERAMA]: Xinerama screens: 2.
[INFO] [XINERAMA]: Saved monitor #0.
[INFO] [Video]: Does not have enough samples for monitor refresh rate estimation. Requires to run for at least 4096 frames.
[INFO] Set config file to : /home/inukaze/.config/retroarch/retroarch.cfg
[INFO] Redirigiendo partida guardada a "/media/Compartido/Videojuegos/Partidas/Emulador/Bateria/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].srm".
[INFO] Redirigiendo guardado rápido a "/media/Compartido/Videojuegos/Partidas/Emulador/Estado/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].state".
[INFO] === Build =======================================
Capabilities: MMX MMXEXT SSE1 SSE2 SSE3
Built: Aug 28 2017
[INFO] Version: 1.6.7
[INFO] =================================================
[INFO] Loading dynamic libretro core from: "/usr/lib64/libretro/mgba_libretro.so"
[INFO] [overrides] no core-specific overrides found at /home/inukaze/.config/retroarch/config/mGBA/mGBA.cfg.
[INFO] [overrides] no game-specific overrides found at /home/inukaze/.config/retroarch/config/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].cfg.
[INFO] Shaders: preset directory: /home/inukaze/.config/retroarch/shaders/presets
[INFO] Shaders: no game-specific preset found at /home/inukaze/.config/retroarch/shaders/presets/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].cgp.
[INFO] Shaders: no game-specific preset found at /home/inukaze/.config/retroarch/shaders/presets/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].glslp.
[INFO] Shaders: no core-specific preset found at /home/inukaze/.config/retroarch/shaders/presets/mGBA/mGBA.cgp.
[INFO] Shaders: no core-specific preset found at /home/inukaze/.config/retroarch/shaders/presets/mGBA/mGBA.glslp.
[INFO] Environ SET_VARIABLES.
[INFO] Per-Game Options: game-specific core options found at /home/inukaze/.config/retroarch/config/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].opt
[INFO] Remaps: remap directory: /home/inukaze/.config/retroarch/config/remaps
[INFO] Remaps: no game-specific remap found at /home/inukaze/.config/retroarch/config/remaps/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].rmp.
[INFO] Remaps: no core-specific remap found at /home/inukaze/.config/retroarch/config/remaps/mGBA/mGBA.rmp.
[INFO] Redirigiendo partida guardada a "/media/Compartido/Videojuegos/Partidas/Emulador/Bateria/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].srm".
[INFO] Redirigiendo guardado rápido a "/media/Compartido/Videojuegos/Partidas/Emulador/Estado/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].state".
[INFO] Environ SET_PIXEL_FORMAT: RGB565.
[INFO] Environ SET_INPUT_DESCRIPTORS:
[INFO] RetroPad, User 1, Button "B (bottom)" => "B"
[INFO] RetroPad, User 1, Button "Y (left)" => "Turbo B"
[INFO] RetroPad, User 1, Button "Select" => "Select"
[INFO] RetroPad, User 1, Button "Start" => "Start"
[INFO] RetroPad, User 1, Button "D-Pad Up" => "Up"
[INFO] RetroPad, User 1, Button "D-Pad Down" => "Down"
[INFO] RetroPad, User 1, Button "D-Pad Left" => "Left"
[INFO] RetroPad, User 1, Button "D-Pad Right" => "Right"
[INFO] RetroPad, User 1, Button "A (right)" => "A"
[INFO] RetroPad, User 1, Button "X (up)" => "Turbo A"
[INFO] RetroPad, User 1, Button "L" => "L"
[INFO] RetroPad, User 1, Button "R" => "R"
[INFO] RetroPad, User 1, Button "L2" => "Turbo L"
[INFO] RetroPad, User 1, Button "R2" => "Turbo R"
[INFO] RetroPad, User 1, Button "L3" => "Darken Solar Sensor"
[INFO] RetroPad, User 1, Button "R3" => "Brighten Solar Sensor"
[INFO] Environ GET_RUMBLE_INTERFACE.
[INFO] Environ GET_LOG_INTERFACE.
[INFO] Cargando archivo de contenido: /media/Compartido/Videojuegos/Emuroms/Nintendo/G.b.a/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].gba.
[INFO] Did not find a valid content patch.
[INFO] CRC32: 0x5a164321 .
[INFO] Environ GET_VARIABLE mgba_use_bios:
[INFO] ON
[INFO] Environ GET_VARIABLE mgba_skip_bios:
[INFO] OFF
[INFO] Environ GET_VARIABLE mgba_idle_optimization:
[INFO] Remove Known
[WARN] SYSTEM DIR is empty, assume CONTENT DIR /media/Compartido/Videojuegos/Emuroms/Nintendo/G.b.a/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].gba
[INFO] Environ SYSTEM_DIRECTORY: "/media/Compartido/Videojuegos/Emuroms/Nintendo/G.b.a/".
[libretro INFO] GBA: Official GBA BIOS detected
[INFO] Environ SET_MEMORY_MAPS.
[INFO] ndx flags ptr offset start select disconn len addrspace
[INFO] 001 M1A1bc 0x7f223a1a4000 00000000 03000000 FF000000 00000000 00008000
[INFO] 002 M1A1bc 0x7f223a1ac000 00000000 02000000 FF000000 00000000 00040000
[INFO] 003 M1A1bc 0x7f223a1f0000 00000000 0E000000 FFFE0000 00000000 00020000
[INFO] 004 M1A1bC 0x7f2233800000 00000000 08000000 FF800000 00000000 00800000
[INFO] 005 M1A1bC 0x7f2233800000 00000000 0A000000 FF800000 00000000 00800000
[INFO] 006 M1A1bC 0x7f2233800000 00000000 0C000000 FF800000 00000000 00800000
[INFO] 007 M1A1bC 0x7f223a1ec000 00000000 00000000 FFFFC000 00000000 00004000
[INFO] 008 M1A1bc 0x7f223a18c000 00000000 06000000 FF000000 00000000 00018000
[INFO] 009 M1A1bc 0x7f223a210ac4 00000000 05000000 FF000000 00000000 00000400
[INFO] 010 M1A1bc 0x7f223a210ed0 00000000 07000000 FF000000 00000000 00000400
[INFO] 011 M1A1bc 0x7f223a210040 00000000 04000000 FFFFFC00 00000000 00000400
[INFO] Environ SET_SUPPORT_ACHIEVEMENTS: yes.
[INFO] CHEEVOS system RAM: 0x7f223a1ac000 262144
[INFO] CHEEVOS save RAM: 0x7f223a1f0000 131072
[INFO] CHEEVOS video RAM: 0x7f223a18c000 98304
[INFO] CHEEVOS RTC: (nil) 0
[INFO] CHEEVOS testing NES (discards VROM).
[INFO] CHEEVOS testing Generic (plain content).
[INFO] CHEEVOS getting game id for hash 9edf4f6e19d901d470aa1117cb0372b3
[INFO] Omitiendo carga de SRAM..
[INFO] Version of libretro API: 1
[INFO] Compiled against API: 1
[INFO] [Audio]: Set audio input rate to: 32884.61 Hz.
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/16bits.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/8bits.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/inu.glslp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/pcsx_rearmed_libretro.so.glslp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/retroarch.cgp"
[INFO] Shader encontrado "/home/inukaze/.config/retroarch/shaders/retroarch.glslp"
[INFO] [Video]: Video @ 720x480
[INFO] [GL]: Found GL context: x
[INFO] [GL]: Detecting screen resolution 1024x768.
[INFO] [GLX]: X = 0, Y = 0, W = 720, H = 480.
[INFO] [GLX]: Found swap function: glXSwapIntervalEXT.
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [GL]: Vendor: NVIDIA Corporation, Renderer: GeForce 6200 TurboCache(TM)/PCIe/SSE2.
[INFO] [GL]: Version: 2.1.2 NVIDIA 304.135.
[INFO] [GL]: Using resolution 720x480
[INFO] [GL]: Default shader backend found: glsl.
[INFO] [Shader driver]: Using Cg shader backend.
[INFO] [CG]: Vertex profile: vp40
[INFO] [CG]: Fragment profile: fp40
[INFO] [CG]: Loading Cg meta-shader: /home/inukaze/.config/retroarch/shaders/retroarch.cgp
[INFO] Found #pragma parameter NTSC Intensity (intensity) 1.000000 0.000000 1.000000 0.050000
[INFO] [CG]: Loading Cg shader: "/media/Compartido/Inukaze/LinuxHome/.config/retroarch/shaders/shaders_cg/TV/gamma.cg".
[INFO] [CG]: Loading Cg shader: "/media/Compartido/Inukaze/LinuxHome/.config/retroarch/shaders/shaders_cg/misc/ntsc-colors.cg".
[INFO] [CG]: Found semantic "POSITION" in prog #1.
[INFO] [CG]: Found semantic "TEXCOORD" in prog #1.
[INFO] [CG]: Found semantic "POSITION" in prog #2.
[INFO] [CG]: Found semantic "COLOR" in prog #2.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #2.
[INFO] [CG]: Found semantic "POSITION" in prog #24.
[INFO] [CG]: Found semantic "COLOR" in prog #24.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #24.
[INFO] [CG]: Found semantic "POSITION" in prog #23.
[INFO] [CG]: Found semantic "COLOR" in prog #23.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #23.
[INFO] [CG]: Found semantic "POSITION" in prog #22.
[INFO] [CG]: Found semantic "COLOR" in prog #22.
[INFO] [CG]: Found semantic "TEXCOORD0" in prog #22.
[INFO] [GL]: Using 4 textures.
[INFO] [GL]: Loaded 2 program(s).
[INFO] [GL]: Using GL_RGB565 for texture uploads.
[INFO] [GL]: Creating FBO 0 @ 256x256
[INFO] [GL]: Creating FBO 1 @ 256x256
[INFO] [GL]: Creating feedback FBO 2 @ 256x256
[INFO] [udev]: Plugged pad: Microsoft X-Box 360 pad (1118:654) on port #0.
[INFO] [udev]: Pad #0 (/dev/input/event5) supports force feedback.
[INFO] [udev]: Pad #0 (/dev/input/event5) supports 16 force feedback effects.
[INFO] [Joypad]: Found joypad driver: "udev".
[INFO] [Font]: Using font rendering backend: freetype.
[INFO] [X11]: Suspending screensaver (X11, xdg-screensaver).
[INFO] CHEEVOS this game doesn't feature achievements.
[INFO] [PulseAudio]: Requested 24576 bytes buffer, got 22272.
[INFO] [Autoconf]: 187 profiles found.
[INFO] [Font]: Using font rendering backend: freetype.
[INFO] [Font]: Using font rendering backend: freetype.
[INFO] [Autoconf]: selected configuration: /home/inukaze/.config/retroarch/autoconfig/udev/Microsoft_X-Box_360_pad.cfg
[WARN] Input device ID 5 is unknown to this libretro implementation. Using RETRO_DEVICE_JOYPAD.
[INFO] Found #pragma parameter NTSC Intensity (intensity) 1.000000 0.000000 1.000000 0.050000
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_favorites.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_music_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_video_history.lpl].
[INFO] Loading history file: [/home/inukaze/.config/retroarch/content_image_history.lpl].
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Unpausing.
[INFO] Trying to write to playlist file: /home/inukaze/.config/retroarch/content_history.lpl
[libretro INFO] GBA Memory: Detected EEPROM savegame
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Pausing.
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Unpausing.
[INFO] En pausa.
[INFO] [PulseAudio]: Pausing.
[INFO] [GL]: VSync => on
[INFO] [GLX]: glXSwapIntervalEXT(1)
[INFO] [PulseAudio]: Unpausing.
[INFO] [PulseAudio]: Unpausing.
[INFO] [Config]: Saved new config to "/home/inukaze/.config/retroarch/retroarch.cfg".
[INFO] Guardando tipo de RAM #0 a "/media/Compartido/Videojuegos/Partidas/Emulador/Bateria/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].srm".
[INFO] Partida guardada en "/media/Compartido/Videojuegos/Partidas/Emulador/Bateria/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].srm".
[INFO] [PulseAudio]: Pausing.
[INFO] Saved core options file to "/home/inukaze/.config/retroarch/config/mGBA/Legend of Zelda, The - A Link To The Past Four Swords (E) (M5) [!].opt"
[INFO] [CG]: Destroying programs.
[INFO] [CG]: Destroying context.
[INFO] [XINERAMA]: Xinerama version: 1.1.
[INFO] [XINERAMA]: Xinerama screens: 2.
[INFO] [XINERAMA]: Saved monitor #0.
[INFO] [Video]: Average monitor Hz: 69.851914 Hz. (25.193 % frame time deviation, based on 2048 last samples).
[INFO] [Audio]: Average audio buffer saturation: 71.46 %, standard deviation (percentage points): 15.37 %.
[INFO] [Audio]: Amount of time spent close to underrun: 0.61 %. Close to blocking: 45.02 %.
[INFO] [Video]: Average monitor Hz: 69.851914 Hz. (25.193 % frame time deviation, based on 2048 last samples).
[INFO] [Audio]: Average audio buffer saturation: 71.46 %, standard deviation (percentage points): 15.37 %.
[INFO] [Audio]: Amount of time spent close to underrun: 0.61 %. Close to blocking: 45.02 %.