With your current normal settings, your 2-channel programs (like CDs in UPSAMPLE that you mentioned) sound good, but 5.1 programs (like audio DTS DVDs like you also mentioned) have too much sub by 6 or 7 dB. Is that correct?

Like Gonk says there are many, many possible combinations of modes that can be used with different sources and connections, but I tried to frame my answer using only the two that you mentioned. I do know that UPSAMPLE can be used with DD5.1, for example, and there are 2-channel synthesized modes for DD5.1 and DTS digital sources, but you are not using any of those. Clearly all the things that the others have mentioned here are also true, like crossover frequencies effecting the perceived bass levels, but so does the room and the subwoofer placement.

In my first email I asked you what two of your settings were, but you only gave me one answer, and now I am not sure which one your answer was for. When your sub level is good for a 2-channel mode like a CD in UPSAMPLE but is too loud for a 5.1 channel mode like a DD5.1 or DTS DVD:
1. What is your SUB level in the full speaker calibration setup menu?
2. What is your 2-channel sub offset?

You need to enter the setup from a surround mode to answer the first question and from a 2-channel mode to answer the second.

I believe the solution will be that you need to set the sub level in the full speaker calibration setup menu (the multichannel one) lower by the 6 or 7 dB you mentioned as being needed, so 5.1 channel programs are balanced. Then you will need to change the 2-channel sub offset so that 2-channel programs are back in balance. The multichannel calibration settings apply to both 5.1 and 2-channel modes, but the 2-channel offset only applies to 2-channel modes. So if you change the multichannel sub level to be 6 dB lower than you have it now, you would end up having to raise the 2-channel offset by 6 dB, in order to bring the 2-channel modes (like CDs in STEREO or UPSAMPLE) back up to the level where you have it now, which is where you like it.

Finally, what Gonk said in his first email is the way to go. Use either the test tones in the 990 or a calibration disk to first set all the 5.1 speaker levels, entering the setup from some surround mode. You can even use the 990's microphone and the AUTO calibration feature. This should make DVDs playing in a 5.1 mode like DD5.1/PLIIx/DTS reasonably well balanced. Then you can listen to a 2-channel mode (a 2-channel source like a CD, the tuner or phono playing in STEREO or UPSAMPLE) and set the 2-channel sub offset accordingly.