[Brian]

If I remember correctly, mail considers the 'only run rules on stuff in the inbox' behavior to be a feature, though other folks may disagree. ;-)

I checked with the lead developer on this, though, and he suspects that this was caused by a bug. He made a change in later builds of OmniFocus, but we suspect that some folks' copies of mail have the old rule cached, though.

To fix this, please try the following:
In mail, select the rule and delete it.
quit mail.
Update OmniFocus to the most recent build available.
Use the Mail preference pane to re-add the rule to Mail.

Can you try that and let us know if the rule starts working as expected?