I suppose it's possible that the amp could cut itself off due to low power earlier than the empeg, the empeg keeps the amp switch line on, so the amp powers off and back on. It's supposed to avoid the thump because the empeg won't have told it to cut on yet, but the empeg never saw the power dip far enough to tell the amp to cut off.

I wouldn't really know how to fix that. Maybe a cap in the amp's constant line? Seems like it'd have to be a pretty big one, though.