Did you just caulk the windows or remove, replace butyl rubber seal, and re-install windows? Have you checked all the clearance lights to see if they could be leaking? Any antenna or other 'holes' in the roof that could allow water in? Weep holes could be drilled out larger if they are the problem.
Bob & Donna
'98 Gulf Stream Sun Voyager DP being pushed by a '00 Beetle TDI