Stupid question, but did you click the 'read'-button on the left side of your inbox ;>? Otherwise it has to be a bug, the only other weird error I ran into so far is getting notified about a new message despite not finding any when looking, simply because the one who sent it deleted it.
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I just logged in for the first time in awhile and I had a message notification. I saw the message and even replied to it (comment on a past giveaway) and the site is still showing a 1 over the message indicator. I scrolled down and clicked through every page of my messages and it's still there. Also tried clearing cookies/cache and no go.
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