When you checked the 4 channels at home, was this through the sled? All I can think of is that the audio connections in the sled have pulled out, losing a couple of your channels - but you'd be very unlucky to suffer from that on *2* channels and only after the drive home!

The thump on startup doesn't sound right; does the amp have a power light? The amp should only power on when the empeg screen comes on. If it's wired incorrectly, then it may be on all the time and you would get a power on thump.

Hugo