Man...wish I saw this thread about a month ago. I have a 03 GT and noticed the same thing you guys are talking about. I have tint on the back, but didnt think that had anything to do with it. I took it to ford, but my weather stripping in the conrner the glass was busted was all scuffed up. I had no idea how it could have got scuffed and of course ford said I probably hit something like a garage door so they didnt cover it. I knew I didnt hit anything, but my car had been to 3 different places within that month for random things and I figured it happened when one of the shops had it. Of course the shops all said they said they didnt, which now maybe I believe them.
Bottom line I had to pay for glass and new tint. Sucks.

amnit:
Oh yeah...I've got that weird clicking noise too, but I wasnt 100% sure where it was comming from. Thats actually how I noticed the glass was chipped/chipping, and I thought perhaps the clicking noise was the glass. I've since fixed the glass and still have the noise.

amnit: again