The simple fact that I can pause the movie a few times and get the issue to go away suggests to me that it is not a re-encoding problem. Will keep you posted. It may very well be that the PS3 is doing it fine and the receiver doesn't like it or handle it properly or something else, but last night I watched The Dark Knight and didn't have the issue at all, where in testing the day before I did - pausing stops it from happening. Weird.
For PCM, if I switch the PS3 from bitstream to PCM and play a lossless PCM or TrueHD track, it comes across not as stereo, but only the two front channels. I read somewhere that this would be the case, so it is working correctly.