Folks, after doing some more reading elsewhere, I am concluding that the problem is likely my Motorola STB for Fios -- although I have not solved it yet. I initially did not rule out the 990, only because it is in the path of both audio and video, and I only started experiencing these issues after installing the 990. But that might turn out to have been a coincidence. I'll keep you posted. Thanks.
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Home Theater Side:
Outlaw 975
Outlaw 7075
Panasonic TC P50ST60 plasma TV
Oppo BD-103 blu ray
LG-LST3510 OTA STB
Channel Master CM-4221 HD UFH antenna
Monster HTS 2600 mk.II power management

Audio Only Side:
McCormack RLD-1 Preamp (has theater pass-thru)
Onkyo CD Player LX-7555
Thorens TD 320 MkII

Speakers:
Vandersteen 1C, VCC, 2Wq
Cambridge Soundworks surrounds