Apps' update status in Market app not always reliable?
I have noticed that I sometimes get a notification that an update is available, but when I go in there, I am unable to update. I, at first, thought that it was some type of syncing issue like you describe, but I have realized ( at least in my situation ) that I have the apps set to update automatically. So I get the notification, but the market actually has already updated the application in the background.

Based on your comments, and if you eventually go in to the market and there is actually an update available for an app that you previously were notified about, then I would say it has to do with how google rolls out the updates. As Chahk discussed, the notifications seem to go before the apps, in some cases. Google does this with just about everything they roll out. Updated in batches.