I have had two Onkyo ht-s790 refurbed units. The first one had a bad sub exactly like you describe. The second had a bad amp in the receiver that would not output any sound through the 'A' speaker out puts (B worked fine). The first went back in return for the second one, and the second is on its way back now. I should have just complained to get the sub returned the first time since everything worked.
The service department is okay, and pretty quick now. It was impossible to get through right after Christmas (it was a gift) but since it has been fine. They pay the shipping there and back every time, and sent out the labels quickly and turn around once they got it was only a day. The worst part is that they have sent me busted units and while yes I am pissed about it, they should be even more pissed. They must have spent well over $200 on freight for it so far and that does not include sending it back. The only people happy with the whole deal must be Fed-Ex.