I can't actually help with a solution but only to say I have had the exact same issue with my 2006 model in the last couple of days.
For what it's worth, I also experienced this in a Golf Mk3 a few years ago. It was never resolved, despite involving the dealer, although topping the auto-gearbox fluid up did seem to alleviate it for a while (but don't overfill).
The clonking didn't seem to do any harm in the longer term except scare the heebie-geebies out of you whenever it happened.
Cheers.
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