Mine does the same and I'm putting it down to the uprated dogbone mount (vibratechnics). I already replaced the flywheel during a clutch change, so it's not that.
You need a long motorway exit to let it over run down from 80ish to 40ish in 6th to feel where in the rev band it's happening. Mine's doing it between 3000 - 2000, slowing down. Everywhere else is smooth.
Now you know why VW use such soggy engine mounts as standard, to mask it ;-) They use a large hockey puck sized mount with voids in it. Very blancmangey and isolates the vibes nicely. If you then replace that with a poly or rubber mount half the size, it can't absorb the vibrations anywhere near as well. It's an age old compromise I'm afraid.
