I've just bought a new case with better cooling than the last and basically just transferred the guts over. Everything is fine in that area except when I switched the PSU back on I got a sort of surge - the fan LED's pulsed, speakers crackled and monitor boinged.

All seems to be fine except my sound. I don't think there's anything wrong with the speakers themselves because another pair I've got also don't work in this PC, and according to everywhere I look (device manager etc) the speakers are plugged in and working properly. Maybe that surge damaged the connector on the mobo?

Yes, I have checked it's not on mute.