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Do you have an iPhone or iPod touch that you also use to read your email? It has been my experience that if I send an email to my +omnifocus address at from my iPod, it will not be handed off to OmniFocus because the Mail app on my Mac won't be the first entity to handle that message, even if I don't actually read the message. If I send to a different account than the one I'm actively using, the problem does not occur.