New windshield has a pucker in the rubber seal.

[Modges'66]

I had the same problem with mine when I first put the windshield in, then I met a glass guy at a carshow that told me to get a Precision Brand seal, and you won't have that problem!... My seal was from LMC, or Brothers, I can't remember. Sure enough, about a year later I got up the nerve to change the seal, and the whole windshield fit in the truck differently. I was totally happy that I took that piece of advise!