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If you use open this page on your phone, then send the email that creates to yourself, you can check the state of the three "BadgeCounts" preferences to see whether OmniFocus thinks it should be adding those items to the badge.

I'm not aware of any other tweaks that would affect that badge, so if those are all set to "1", this should be working as you expect. If that's not what you're seeing, please forward that debug info along to our support ninjas; we'll be happy to investigate this with you and get things straightened out.