USB Joypad stops working after Menu Screens in PSX Emulation

I’m currently running RetroPie 2.6.0 on a RPi2. I’m also using the iBuffalo usb joypad, and after some menu screens in the PSX emulator (it varies on how many screens there are in the game) the joypad stops working. At this point, I can only control the game with a keyboard. When I first load the game the joypad works fine. Has this happened to anyone else? Anyone have any ideas on how to fix this?