Connection Issue?
Sounds like it could be a connection issue, however I'm not sure if it's external (wire from sp. to receiver, wire from receiver to sp., etc.) or internal (amp/logic board wiring issue). Do the test tones work fine to all speakers?
If it were a heat issue, the receiver would completely shut down, not just a few channels.
Just for my own sanity, I would un-seat and re-seat all of your speaker connections just to be safe. Make sure the receiver is turned off when doing so. If this is only in 5 channel stereo (e.g., all channels work fine in DD/DTS), it could be an internal issue. I say this as it sounds vaguely familiar to an issue I encountered some time back w/a receiver and the sub out, it was doing almost exactly what you mentioned and it turned out to be a bad solder job on the logic board to the sub pre-out. -TD