[whpalmer4]

It's probably worth verifying that this is a problem on OmniFocus' side of the fence, so to speak. Remove the part of the rule that invokes the script and replace it with something that moves the message to a different folder or flags it or otherwise indicates that the rule was successfully invoked. If it still isn't happening, now you know it is a Mail issue and not something going wrong in the handoff to OmniFocus.

Is this something that used to work, and no longer does, or you've never had it working?