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You may want to try the troubleshooting steps here:

http://www.omnigroup.com/support/omnifocus-mtn-lion

We recently submitted an update to Apple that addresses issues with the Mail Rule and Clip-O-Tron in Mountain Lion, but they need to review and approve the update before it can be made available in the Mac App Store.

Feel free to email us if you're still having trouble. Thanks!