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It is possible the transmission is learning. After you reprogram the PCM, the transmission needs to learn how to behave. This is from one of Ford's TSB's.

 

"PLEASE ADVISE THE CUSTOMER THAT THIS VEHICLE IS EQUIPPED WITH AN ADAPTIVE TRANSMISSION SHIFT STRATEGY WHICH ALLOWS THE VEHICLE’S COMPUTER TO LEARN THE TRANSMISSION’S UNIQUE PARAMETERS AND IMPROVE SHIFT QUALITY. WHEN THE ADAPTIVE STRATEGY IS RESET, THE COMPUTER WILL BEGIN A RE-LEARNING PROCESS. THIS RE-LEARNING PROCESS MAY RESULT IN FIRMER THAN NORMAL UPSHIFTS AND DOWNSHIFTS FOR SEVERAL DAYS."

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If you were to bring it back to the dealer for a second glance over.... I would expect for them to keep it at least 1 day in order to be able to drive it around in order to recreate what it is that you're currently experiencing.

 

I would agree with EBB though.... different strategy for the ECM, or hell, ask 'em to return to what it was previously so that you now know the distinct differences between the two.

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Both tuner tune packages change tranny shifting parameters. However, I am running a new Flex strategy code from FORD.. System is completely stock except for smaller tires & much lighter wheels. My tranny is shifting great, and quite similar to the tuned versions, at least in normal driving. Haven't noticed any searching or slow downshifts in around 2,000 miles in last 3 wks.

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