hey, I have the same thing happening but not all the time,
I can't find the where its coming from but Ive never had any problems with the top working or leaking (knock on wood)
I have a 2000 Formula Red S2K I rescued her from bad home and thought that the top was going to be the first thing I needed to replace.
she may squeak alittle but thats about it

These cars are thought out and built really well one of the finest street cars around I love this car