I've had this happen on both MkV and MkVI cars, including the fixing itself. Tried realigning, as per the manual, in the MkV and it fixed the problem but returned a few months later. Also had the dealer look into it, just in case but they found nothing unusual (and then reset the windows anyway just to be sure). Eventually I just gave up fixing it as it always went away after a day or two.

Also, when using the remote to make all the windows drop I found that most of the time at least one rear window didn't drop - always a rear, never a front. It wasn't connected to the alignment issue as it didn't always line up with the timing of both issues.