i wonder if in your different inputs in the 990 menu you have have selected something like Stereo as the default, instead of maybe DPLII? that would cause only certain speakers to come on when switching inputs from Video 1 to DVD. Check your default settings for EACH input.
good luck man.. that is the only thing I could think of.
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Outlaw Audio 990 pre amp
Adire Audio sub (SVS 12.2 driver)
CAL Alpha tube DAC
Parasound P/HP-850 2 CH pre
Pioneer PL-530 TT
Polk Audio SDA 2B
NAD 2600A amp
Danger Boy here