FYI
I'm still using SW 2005 SP5.0 and I've had the same problem for years. It appears at random, mostly when I have a large assy (>100 parts). I have a Nvidia 4500 which is a top of the line video card and I have always run the correct driver. Never figured it out, just learned to live with it. Do your affected faces sometimes temporarily go back to the correct display as you pass the cursor over it? Mine act this way. Sometimes running a macro to remove all colors assigned to faces will correct it for a while.
Timelord