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The iOS 5 update appears to sometimes turn various apps' icon badges off - which ones this happens to seems to be somewhat random. We're seeing other developers report the same issue with their apps; hopefully it'll get fixed in a future iOS update.

In the meantime, just open the Settings app on your phone, tap into Notifications, then make sure OmniFocus' "Badge Count" setting is set to "On". (Ditto for any other apps affected by this.)

Hope this helps!