Maybe you have to configure the controllers as "CD32 joypad" or "gamepad". WinUAE behaves differently on gamepad: third button is active. On CD32 joypad setting, all buttons are active (I suppose that you have a punch button issue only)
I just tested the game out on another windows computer with retroarch. The game does not like other controllers than X360 controllers. I think controllers without a second thumbstick error out the controls. I know AGS fixes this issue somehow. When 3.1 comes out hopefully it will include this game and fix this issue.