So, you keyboard works without problem in the menú (Example, you configure the key Q as Start, etc…, and in the menu Works but in, for example, the SNES emulator the Q did not work as Start button?)
Did you tryed to re-configure again your keyboard from Main Menu\Configure Imput? (To Access to the Main Menu you need to hit your Start key configured on the first boot of the Retropie system)
Here you can see where the emulators store the config files https://github.com/RetroPie/RetroPie-Setup/wiki