Electrical problems are a pain in the ass and sometimes don't tend to make any sense at all. The speakers in my Spyder stop working as soon as you raise the top up half an inch, but otherwise work flawlessly all the time with the top down. No reason for it, it just happens.

I would just trace all the wires as far as you can for any loose ends or bad connections. I have to tear the entire insides of the Spyder out to hardwire the speakers.