hmm, how about disabling joystick support?
try the command "in_initjoy 0" from the commandline when starting quake (quake2.exe +set in_initjoy 0), further you should disable psx-joypad support as well, see amiga-quake2 readme, it probably tells you how to do it......
it worked for q1 that way, i remember having the same problem...
