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I've got the same problem but after 10-14 days of no car use. I also have an aftermarket head unit (Alpine SatNav/Audio DVD).
On OEM Mk5 GTI's there's a known issue of "Radio" battery drainage but VW released a software update to cure it. Problem is that it only applies to OEM.
We've so far identified the drainage to Fuse 19 in the engine bay fusebox. The GTI Handbook identifies the F19 as "Radio".
We're still investigating and will share here what we discover. Likewise I trust you'll do the same