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I am trying to play this game with an xbox 360 controller for PC. I got the joystick settings right where I wanted them by tweaking the configuration settings and I am using the built-in DOSBox keymapper. I had set A to be Alt and B to be Space (Alt is jump, Space is shoot). However, when I did this, pressing either button caused Jazz to jump AND shoot at the same time, every time.

I tried changing the bindings so that RB is space/shoot and A is Alt/jump. This makes it so I can shoot without jumping, but pressing the jump key still causes Jazz to shoot. Not sure why this is happening.
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Solved it! Apparently, the game will automatically read the Xbox controller as a game pad and automatically assigns functions to the buttons. B is automatically the shoot button, A is the jump button and X is weapon switch. The only issue is that X is a bit fussy and doesn't always work, but other than that the game controls well.

I think the issue was trying to alter the keybindings via the DOXBox binding tool.