If it was updated in Jan I would suspect it is on 'CL' calibration which I believe is the most upto date. This was to improve cold starting/idle speed I believe amongst probably other things Ford dont want us owners to know about.

Unless is was a incomplete update which I doubt I suspect there is another issue such as boost solenoid. I appreciate your under warranty but I would only take it to a dealer who you trust with decent techs. Failing that take to a specialist ;(

HTH...