The symptom is that when I turn off the ignition there is a loud thump and the unit shuts off completely.

Strange. This sounds like the negative spike bug. But that's not supposed to happen on Rio-brand players. And it only happened when you upgraded to 2.0b3.

Please write the empeg support team directly about this and get a dialogue going with them. If it's a software issue, they will sort it out for the next release, but I would guess that they need to speak directly to someone with the problem.