So I just got home from Samys in Santa Ana where I was going to pick up a wet clean setup (after noticing my sensor needed cleaning). The guy there (Ken, about the only one I've met who's remotely knowledgeable/helpful) had me test out a loupe, and much to my surprise I not only saw the dust specks that wouldn't blow off but we also found about 3 scratches running lengthwise on the LPF. Crap.
The camera was in at CPS in October for the mirrorbox replacement/recall thingy. I am thinking that they did the damage to the LPF. If the damage was already there, wouldn't they have noted it on the work form?? Calling Canon tomorrow, but I want to be prepared to get some good help.