I added a tri-mode crossover and a sub woofer this weekend, and whilst it has improved the sound in car a great deal, I now also have the "thump" problem too! This is now occurring when I power on the unit, so I get *thump* when the ignition comes on, followed by *thump* when the empeg decides it should be in power-down mode. So my wonderful theory about MOSFET charge storing on the amp input is most likely a lot of b******s. Funnily enough, it does not occur on power down or ignition off, but I have a pretty tiny amp.

Looks like I will be wielding the soldering iron sometime soon.