By the way, in the case of one of the CD32s it was a dodgey PS/2-AT adapter in the AUX port I was using for an A2000 keyboard that caused the problem, so it's not just the joystick ports that can harm your Amigas.
I had an sx1 giving some problems closer... i discover it playing super stardust cd32 version using the sx1 rgb output for better picture quality, with sx1 connected extra buttons of the cd32 pad were ignored.