It's most likely the tune. A buddy on the Roush forum had his 2010 vert, with a M90 and new tune from VMP. His is an automatic. He takes it into local ford dealer, and no way in hell could they figure it out. AC would not come on. In desperation, he loads his older JDM tune ... and presto, AC is now working. Swap back to the VMP tune..and AC went dead.
I had VMP tune my 2010 Auto ( same M90 blower)...and presto, my AC went dead. Notified VMP, and got a revised tune, fixed in 3 mins flat.
Then a year later, a fellow from the caribbean complains his 2010 auto, ( M90 blower) with a new tune, AC went dead. ( different tuner, forget who). Same deal, something in the tune got missed. Dunno why it was always a 2010 auto with M90 blower in all 3 x cases. Easy fix though. There is some table or similar in the tune somewhere, that turns the AC on /off. Start there, b4 you tear your hair out.