Haven't had this problem myself thankfully, although whenever I have a game update available, it shows as still available for hours or even days after I download the update and the account refresh never seems to do anything about it for me. Eventually the misplaced flags correct themselves at a random time, although it is usually within 2-3 hours or so I would say.

I plan on re-downloading my entire catalogue of games (429GB currently) when GOG Galaxy launches, spread over probably 2+ months of time though, so if the glitch does strike, I'd probably just wait until then to "fix" it. :)

Me too, about 2 weeks ago.
Clicked them all too.

I would purchase one, if not for the fact that my bank's records of deposits have been erased, will this never end?

And I bet you had as much fun as I did. ;-P