Couple of weird things I noticed:
Robocod AGA (WHDload) doesn't work at all with this controller! At least no fire button input is detected to start the game, I'm sure it worked with the pad.
AmiMasterGear, could never get the second button input to work, either with the CD32 pad or the sega pads, no matter what options were used.
With the joystick this now works perfectly, not sure if it has something to do with microswitches making a better contact than the carbon pads of a joypad.