you could try to change your pad to an original amiga pad or joystick. For some reason I've had trouble getting my cd32 pad to work with certain games. The same with my megadrive2 pad. This doesn't happen very often though, luckily....
It's a long time since I used Amimastergear and that gameboy emu, but I can't remember having any problems with them. Really fast emulators too....
