Yup! It's a well known issue on the MK5! Next time you get the thrumming noise, crack the roof back a notch or two and / or drop the window a bit, if the noise goes, there's your issue!
The MK4 had a lovely notched wind deflector to kill the turbulence, but for some strange reason VW fitted a plain one on the MK5. I did post a thread on here ages ago if anyone had attempted to fit a MK4 deflector to a MK5 but it drew a blank.