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Yes, the tranny has an adaptive learning cycle it goes through. The most critical stage of this process is right after the ECU has been reflashed or the batterires have been disconnected.
The transmission must completely relearn and adjust line pressures.
The quickest way to get the tranny on its feet after a reflash is pretty simple.
After startup, while idling (foot on brake), shift from Park to Reverse, Reverse to Neutral, Neutral to Drive, letting the tranny fuly shift into gear each time. Then go from D to R, R to P, P to D. Repeat this a few times in different combinations. You truck will drop into gear more quickly and more positively each shift.
To the OP, what you're probably seeing is the tranny smoothing out the shifts after having a chance to adjust. It's probably not any slower, just smoother.
06' F-250 Harley Davidson CC SB #19
6" lift, tuned, intake, exhaust, gauges, on 37x13.50x20 Nitto Mud Grapplers
Sinister RR, Powermax, Liberator Solid-Y pipe, GoGo Stage 1.
Still to do: ARPs, ADII, Hellman Sump