Doug:

Here's what I tried. Set input Video 1 to Upsample and input Video 2 to PL II (or IIx if you have 7.1).

Get out of the menus and set the source as Video 2. Go back into the menus, go to Calibration and start your sub tone. Use an SPL meter to note the SPL's. Then move the calibration level for the sub up and down. Notice how the SPL's change?

Now get out of the menus, switch the input to Video 1 (Upsample). Go back into the menus and go to Calibration. When I move the calibration level for the subwoofer, the SPL's don't change at all. I can move the sub level in the cal menu to -15 or +15 and the actual SPL's of the sub in this input with Upsample do not change 1dB.

Could you test this with yours and see if it does the same thing? I'd be interested to see if yours works as expected - i.e. the sub calibration level works on all digital inputs no matter what the "surround mode" for that input is