I was just thinking that on a few occasions I plugged my floppy drive (or possibly it was the LED lines - cant remember it was over a decade ago) in the wrong way around and it caused the floppy LED to light up permanently (the drive was still operable during this - ticking/reading disks etc) and wondered if something similar might be occurring.
I've only seen that with 5 1/4" floppy drives on a pc as the connector wasn't keyed. In that circumstance the drive wouldn't work.
So it must have been the led cable, although if it's an a500 then isn't that part of the keyboard? Plugging that the wrong way round could to it I suppose. I haven't opened up any other amigas recent enough to remember if they had seperate wires for the leds.