Here's an update. After about 5 days at the dealer, they have come back to me telling me this is a "glitch" in the control software and Ford Engineering has no fix. Basically with the dual zone climate controls, and maybe others, the recirc door opens when you shut off the ignition. This is supposed to help with door bounce due to the better sealing in the Gen2 Cab. When you start it back up, the recirc light may be on, but the door stays open. You must "double click" the recirc button to get it to close. Must be another microsoft product like Sync!
Give me three knobs (fan speed, temp, where it blows) like my GEN 1 trac and i'll be happy!