We had problems with a datacenter test that left our caching layer in a partially broken state.
All issues should now be resolved.
Also, see https://meta.stackoverflow.com/questions/268957/topbar-notifications-dont-go-away
It is a feature (not bug) and the graphics below will illustrate why:
Note how the discrepancy in count is explained by the red text in the top graphic.
Personally, I think the top Unanswered button might be better named something else to avoid confusion - perhaps Priority because we do not want good questions to go unanswered; good answers to go un-...