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How do you know the rules are being run at all? What you describe is consistent with them not being run, and it is difficult to imagine a scenario where OmniFocus would act differently upon the emails depending on whether the rule was invoked automatically or manually.

First step is to establish that the rule is being run. Insert an action at the top of the rule to play a sound or bounce the icon in the dock. Send an email. If the email shows up in your mailbox, but you don't get your sound or bouncing icon, make sure that nothing is marking that email as read before Mail gets it. Mail only runs the rules against what it thinks are new, unread messages.