It's either to low for home theater and to loud for 2 channel listening. Not sure if this is the problem or not.
You may want to try dailing it in for home theater and then using the two channel sub offset to dial it down for that stereo listening.
What i noticed is that there is no difference in the DD and DTS settings. The pre doesn't remember different settings for both formats.
The 990's channel calibration is global - while DD and DTS do sound different, the two should not vary between individual channels (DTS is generally about 4dB louder across the board, but that may vary somewhat from disc to disc depending on how the DD and DTS tracks were mastered). I've generally had good results using the 990's internal test tones for channel calibration.