I wish I had the answer, but unfortunately all I can do is affirm that yes, this happens because HDMI is a poorly implemented "committee standard" that unfortunately introduces problems while solving for others.

To give you an example, if I run my Mac Mini DVI>HDMI direct to my TV's HDMI in, the picture is a perfectly clean 1280x720. If I run it through my pre/pro's HDMI switching, the mac and TV both say it's 1280x720, but it has a black bar around the edge of the screen and the sync is off, making it look soft.

Try running your HDMI cable direct from your blu-ray to your projector; whether it works or not will tell you if the 990 is introducing the problem.