Well, I played around with this last night. In case anyone's interested, here's what happened.
I unplugged the subwoofer and the thumping went away...there is no thump through any of the main speakers, just the sub.
I plugged the sub back in and the thump was back. As with Gary, it happened when switching from any digital source to any analog source, whether a component was connected or not. I did this with the TV both on and off.
While my sub is 5-6 years old, I have never had a problem like this with it initially plugged into a Yamaha DSP A-2070, and then a cheapo Sony Dolby Digital Receiver.
I guess I'll try a different sub cable (grasping at straws here) and if that fails contact Outlaw.
Could the setting of the main speakers to large have any effect on this? I wouldn't think so, but it would be easy enough to test.