Very interesting.....I've had the same thing happen. Often, for now apparent reason, 5.1 DD is broadcast in stereo, then the commercials are broadcast in surround and normal programming goes back to stereo. Always thought that was strange, but since it also happened with my previous AVR, didn't think it had anything to do with the 990. I notice most often on NBC nightly news and NBC national HD golf broadcasts in Sacramento.
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B&W 804s mains
B&W HTM4 Center
Outlaw 990
Anthem MCA 30 AMP
Audiosource Stereo AMP
Monitor Radius 180 surround
Comcast DVR
Sony HX929 LED TV
Apple Air Express/Apple TV