Email Rules Work, but are not automatically triggered
 

I have two mail rules built around the MailAction.applescript. The first is generated by OmniFocus itself in preferences, the second I created based on that one.

They are both placed at the very top of my rules list and should be run first on every incoming email.

However, they are _never_ triggered automatically. No matter what, the emails are not added to omnifocus.

I can select the emails, right click, and choose "Apply Rules" and everything works as expected.

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.

Well, the issue was I knew they were _not_ being triggered at all. Not that I thought the rules were not working _when_ they were triggered.

I found the problem, I do filtering in gmail and mails are sorted into subfolders server side.

I found out Mail.app does not run rules on anything but mail in the Inbox. Haven't found a solution to that yet.

How about filtering messages destined for OmniFocus into a separate folder, then having an Applescript run from iCal every (insert your desired interval) that takes the contents of that folder and does perform mail action with messages with the rule to process them? Or can you simply not filter the OmniFocus messages?

Those are some good ideas, didn't think of the ical option at all. I was going to write a launchd.plist that ran periodically, but ical seems easier.

One of the issues is I was going to monitor emails from some of the regular stores I buy from online such as amazon and bill notifications. So, not sorting isn't really an option but an ical event that ran a script would work super!