Hello Whiskey,
Based on your description, it appears that the Auto Setup routine was unable to accurately determine the subwoofer distance. You can confirm this by going into the Model 990's channel calibration menu. There, you will want to observe the delay setting for your subwoofer. Instead of a numerical distance, I'm guessing it may have "letters" instead of an actual distance.
If so, change this to the actual subwoofer distance. This will resolve your current lip sync delay issue.
Best,
Scott