I may have an idea...

In the 990 channel calibration setup menu, what is your current sub level in dB for multichannel? What is your current 2-CH offset when UPSAMPLE sounds right?

How many dB do you need to turn down your sub for DD/DTS to be correct?

On yeah, are your front speakers set for SMALL or LARGE? If you are set to LARGE, there may be more questions!