Controller not working in JPCSP

[nyanderes]

Hello! I mapped my keys and I'm using the PS2 mode (motioninjoy) however when I go into a game the controls don't work. The opening started to play and it was immediately skipped even though I didn't press anything. Basically my controller is not working properly and for some reason does things by itself sometimes. The keys that I originally mapped do not work, for instance if I try to press start to skip the opening it does not work.
I also tried the Xbox 360 mode and the exact same thing happened. My version of JPCSP is up to date and my controller does work on everything else.