if you are using UAE,
try setting the controllers to "gamepad" instead "joystick"
Viewing post in Double Baboon Ninja jam comments
No I even deleted and reinstalled the game on my CF card and I start it up with 2 button joystick in the joystick port and mouse in the mouse port and yet every time i start the game it's skipping by itself through the intro as if a button is pressed, then not allowing me to jump when game starts. If I use my CD32 controller (even if I do hotswap it following the above), I can fully control the game normally. So I assume something in the game settings thinks I'm using a CD32 controller at all times.
All other games/programs behave normally.