My wife's Passat was doing the same thing recently. I pulled the rotors off and took them to O'Reilly's to get them turned. When I picked them up, they were worse than before. After much back and forth and my insistence on investigation, it turns out their machine had a bent shaft. Comp'ed me two NEW rotors (they should have).

Have you run through a water puddle recently while the brakes were warm? That'll do it every time.

Jason