I am having the same problem as well. I upgraded to Itunes 10.6.7.1 a few weeks ago. I have two PC laptops that I use, one for general use, and one for DJing. I manage my itunes on my main computer, and basically clone my library before I have a gig, so that my itunes folder (which serato reads for my playlists and stuff) is identical to the computer I use daily.
I noticed recently, that i'm getting the grey exclamation points on tracks that I definitely did not delete. When I look for the files, they are completely missing from my external hard drive. Some tracks are also copying themselves. But the tracks I am looking for, GONE. No trace. They remain on my ipod, because I haven't synched in a while, but they are no where to be found on my hard drive. Luckily I had backups of some of the files, and were able to just drag them into itunes, and it's like nothing ever happened, but not for all of the tracks. And it's annoying to find new ones every time I open Itunes. ***??!?!?
Why are we getting no answer as to why this is happening, and why isn't there a fix???! This is wedding season, and I hate to look for a track and find that it is missing for no reason at all, when I am doing a gig. Or just in general.