I compiled RetroArch myself on a Pi 2 running Arch Linux.
After lots of messing around, I got it to run at full speed, yet my audio lags about 250ms (guessing) behind the video. For example, in Super Mario Bros on the NES, the jump sound effect plays only after Mario lands on the ground.
I’ve enabled audio sync, which did nothing to help, and I’ve tried various settings to no avail.
Does anyone have any advice? I’m so frustrated with this, I’ve been trying to fix it for days. 
Here’s my config file:
config_save_on_exit = "true"
input_max_users = "5"
input_menu_toggle_gamepad_combo = "0"
input_axis_threshold = "0.500000"
ui_companion_start_on_boot = "true"
video_gpu_record = "false"
input_remap_binds_enable = "true"
back_as_menu_toggle_enable = "true"
netplay_client_swap_input = "true"
input_descriptor_label_show = "true"
autoconfig_descriptor_label_show = "true"
input_descriptor_hide_unbound = "false"
load_dummy_on_core_shutdown = "true"
builtin_mediaplayer_enable = "false"
builtin_imageviewer_enable = "true"
fps_show = "false"
ui_menubar_enable = "true"
suspend_screensaver_enable = "true"
libretro_directory = "~/.config/retroarch/cores"
libretro_info_path = "~/.config/retroarch/cores"
content_database_path = "~/.config/retroarch/database/rdb"
cheat_database_path = "~/.config/retroarch/cheats"
cursor_directory = "~/.config/retroarch/database/cursors"
rewind_enable = "false"
audio_latency = "64"
audio_sync = "true"
audio_block_frames = "0"
rewind_granularity = "1"
video_shader_enable = "false"
video_aspect_ratio = "-1.000000"
video_aspect_ratio_auto = "false"
video_windowed_fullscreen = "true"
video_scale = "3.000000"
autosave_interval = "0"
video_crop_overscan = "true"
video_scale_integer = "false"
video_smooth = "false"
video_threaded = "false"
video_shared_context = "false"
video_force_srgb_disable = "false"
video_fullscreen = "false"
bundle_assets_extract_enable = "false"
video_refresh_rate = "50.000000"
video_monitor_index = "0"
video_fullscreen_x = "0"
video_fullscreen_y = "0"
video_driver = "gl"
record_driver = "null"
camera_driver = "video4linux2"
location_driver = "null"
threaded_data_runloop_enable = "true"
dpi_override_enable = "true"
dpi_override_value = "200"
menu_driver = "rgui"
menu_pause_libretro = "true"
menu_mouse_enable = "false"
menu_pointer_enable = "false"
menu_timedate_enable = "true"
menu_core_enable = "true"
menu_dynamic_wallpaper_enable = "false"
menu_boxart_enable = "false"
video_vsync = "true"
video_hard_sync = "true"
video_hard_sync_frames = "3"
video_frame_delay = "0"
video_black_frame_insertion = "false"
video_disable_composition = "false"
pause_nonactive = "true"
video_swap_interval = "1"
video_gpu_screenshot = "true"
video_rotation = "0"
screenshot_directory = "~/.config/retroarch/screenshots"
aspect_ratio_index = "19"
core_updater_buildbot_assets_url = "http://buildbot.libretro.com/assets/"
core_updater_auto_extract_archive = "true"
camera_allow = "false"
cheevos_enable = "false"
cheevos_test_unofficial = "false"
audio_rate_control = "true"
audio_rate_control_delta = "0.000000"
audio_max_timing_skew = "0.000000"
audio_volume = "0.000000"
audio_driver = "alsathread"
audio_enable = "true"
audio_mute_enable = "false"
audio_out_rate = "48000"
location_allow = "false"
video_font_size = "32.000000"
video_font_enable = "true"
ups_pref = "false"
bps_pref = "false"
ips_pref = "false"
system_directory = "default"
input_remapping_directory = "~/.config/retroarch/remap"
audio_resampler = "sinc"
savefile_directory = "default"
savestate_directory = "default"
video_shader_dir = "~/.config/retroarch/shaders"
video_filter_dir = "default"
audio_filter_dir = "default"
core_assets_directory = "~/.config/retroarch/downloads"
assets_directory = "~/.config/retroarch/assets"
dynamic_wallpapers_directory = "default"
boxarts_directory = "default"
playlist_directory = "~/.config/retroarch/playlists"
rgui_browser_directory = "default"
rgui_config_directory = "default"
rgui_show_start_screen = "false"
menu_navigation_wraparound_horizontal_enable = "true"
menu_navigation_wraparound_vertical_enable = "true"
menu_navigation_browser_filter_supported_extensions_enable = "true"
menu_show_advanced_settings = "true"
menu_entry_normal_color = "ffffffff"
menu_entry_hover_color = "ff64ff64"
menu_title_color = "ff64ff64"
content_history_path = "~/.config/retroarch/content_history.lpl"
content_history_size = "100"
joypad_autoconfig_dir = "~/.config/retroarch/autoconf"
input_autodetect_enable = "true"
overlay_directory = "~/.config/retroarch/overlay"
input_overlay_enable = "true"
input_overlay_enable_autopreferred = "true"
input_overlay_hide_in_menu = "true"
input_overlay_opacity = "0.700000"
input_overlay_scale = "1.000000"
osk_overlay_directory = "~/.config/retroarch/overlay"
input_osk_overlay_enable = "true"
video_message_pos_x = "0.050000"
video_message_pos_y = "0.050000"
gamma_correction = "false"
soft_filter_enable = "false"
flicker_filter_enable = "false"
console_resolution_width = "0"
console_resolution_height = "0"
flicker_filter_index = "0"
soft_filter_index = "0"
current_resolution_id = "0"
custom_viewport_width = "1440"
custom_viewport_height = "1080"
custom_viewport_x = "240"
custom_viewport_y = "0"
video_font_size = "32.000000"
block_sram_overwrite = "false"
savestate_auto_index = "false"
savestate_auto_save = "false"
savestate_auto_load = "false"
history_list_enable = "true"
fastforward_ratio = "0.000000"
slowmotion_ratio = "3.000000"
sound_mode = "0"
state_slot = "0"
user_language = "0"
custom_bgm_enable = "false"
input_driver = "udev"
input_joypad_driver = "udev"