I just got a problem like this fixed on my A4000D motherboard over the weekend.
The capacitors on my board have been replaced by the non-polarized type.
However, upon putting everything back together, the sound on my A4000 was still
terrible. After 7.5 hours of messing around with the hardware (different
motherboard, accelerator, removing expansion cards, removing Zorro expansion
daughter board), my dealer and I found the problem. It was as simple as the
-12 volt and it associated ground wire not making proper contact in the main
6-pin motherboard power connector. When I plugged that in after the capacitor
change, the -12 volt and its ground got pushed out of the connector somehow so
they weren't making contact. The op-amps (operational amplifiers) that produce
sound on the Amiga require -12 and its ground in order to function properly.
Without either one, the sound output is very bad. We connected the main power
connector and then wiggled and pushed in the wires with a pair of needle-nosed
pliers. After that, perfect sound from my system!