I purchased a 2004 525I back in April since then i had all 4 of the windows seal serviced twice the last one just recently (about 2 days go) and the noise is back again. It's a rubbing sound. Has anyone had this problem? Was it ever resolved. It mostly happens when going over bumpy roads hardly ever when traveling on a smooth road. Thanks

 

Most of the early E60's did, some problem with the door seals, it has been heavily discussed in this forum. Basically they creak like a Spanish Galleon with these seals.
Changing the door seals should take care of it. At least for some time.