Enemy,
I had decoding issues as well with my 990.
What solved it for me was plugging the 990 into the "Digital" power outlet in my monster HTS-3600 (I think that's the model number, not near it at the moment...).
If I plug it into another port, I'll start getting DD decoding issues. EXACTLY what you describe with...
"Ok, I just found another strange PLIIx issue. I just had DISH installed today and was testing my setup. I had it on 9477 with the documentary "Hard Water" playing. INFO says it has a DD 5.1 soundtrack. Playback in regular Dolby 5.1 mode confirms this. If I switch to PLIIx Movie mode, then it loses the left and right side channels, but the rear left and right playback just fine (so basically it is just switching the side surrounds to the back surrounds). If I switch to PLIIx Music mode, then all 7 channels work."
EXACTLY. I swear, a good power filter and it cleared up for me. I called monster and they stated that the "Digital" is the most filtered, followed by the Analog, and down from there...