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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.