OK, check this thread for discussions about similar problems to yours:
In particular, I’d try the watch command from that thread, which will show you the GPIO activity, and my give you some more clues.
A couple more questions…
1 Are you using a standard image, downloaded from the RetroPie web site?
2 Have you done an update on the system (RetroPie > RetroPie Setup > Update)? If not, I’d uninstall the picade software, reboot, do an update, reboot, re-install the picade software, reboot.