In general, if one sets the delay in the DVD, and that delay happens to be more than needed, then the 990 will not be able to compensate, as it can only apply a delay, not an "advance".
As a rule of thumb, as rance suggets, don't apply the sync delay in two places.
Abandon all the adjustments made in the DVD player and do them all in the 990.
In general, my eperience with the 990 showed me that its auto calibration is not stellar. It got put on the wrong path by the wall refeactions, in my case.
In my experience, nothing beat a tape rule for distances and an SPL meter for levels.
Other than that, I find the 990 to be a superb piece of equipment.

Just my two cents...