Sync Failure - Then it works?
 

Often I start Omnifocus with a clipping action from Mail in Mountain Lion. When I do this, I get the "!" in the sync icon. If I click on this again, the sync works. Any idea what is going on?

On 10.8.something, OmniFocus started having trouble accessing the keychain if it was launched from a service.
This sounds like a symptom of that issue, since the main thing OmniFocus stows in the keychain is your sync account info.
Until we can work with Apple on a proper fix, the main workaround would be to keep OmniFocus running, but minimized, rather than quitting it when you're not using it.