I have had the 990 lose the front L/R channels when going from a 2-channel mode to a multi-channel mode on the same input. I have never experienced waht you are describing though. I got around the issue of the L/R dropping out by connecting the optical cable to the DVD input and the coax cable to the CD input (both from the DVD player as I use it for movies and CDs). Then I set the CD input to default to upsample and the DVD input to default to DPL2X.
Come to think of it, I don't even think I have tried doing what you described. Any time I use upsample, it has always been with a 2-channel source. I will try with a 5.1 disc and get back to you tonight.
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Doug
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