We had a similar issue with the window in our 2006 VW New Beetle Convertible. Window came unglued. Took car to a very good upholstery shop here locally and the owner told me that on many of the European-source convertibles, the EPA made the manufacturers switch glues on models during this time frame (i.e., 2002 - 2009). Don't remember reason why. The new glue didn't hold up in warm climates. Anyway, that's what I was told and he has always been straight with me. And he does a lot of convertible tops around here.

He recommended a replacement top including window from a California vendor. Told me that that top was of highest quality and came with a 15-yr guarantee for workmanship. Ended up costing me $2100 (top = $1400; install = $700). And the top is superior to the typical VW top installed for those model years.

I don't here any of the newer convertible Beetle owners complaining about windows coming loose. VW must have figured out a gluing solution and/or made a design change to this area.