First, I'd like to thank everyone for their input.
Second, let me tell you what happened today. I took a day of leave from work, actually several days, so that I could get a jump on the holiday weekend (Columbus Day for my friends across the water). I took the bike back to the shop. My mechanic told me that he never removed the back wheel from the bike, nor did he interfere with the rear brake, aside from checking pad wear, fluid levels, and such.
The service mngr (I expressed my feelings about him in an earlier post) took it for a test ride and surmised that the problem is a result of a worn rear tire. He says that because the compound has worn down, it causes the back wheel to lock, when using the back brake, because there is not enough rubber to properly grip the road when attempting to stop. As a result, he says, the wheel locks and the chain jumps because the counter-something-or-other is still moving. He feels that the "thump" sensation is coming from the chain, jumping or moving or dancing or whatever he said. He also said that all of the mechanical braking components appeared to be working fine. He based this on his visual inspection and test ride (using only the rear brake to haul the beast to a stop)
Does this sound like it could be the case? Or should I go back and punch him in the mouth. Maybe a bitch slap would be better. Or, on the other hand, should I thank him for a proper diagnosis?
BTW, I'm on my 3rd set of tires on THIS bike and I never had a problem like this on the previous two sets when they were toward the end of their usable life.