Yes, there is a reason, and a very simple solution. Our cars have what is called "Adaptive Learn", which means that the the car learns how you drive, and adjusts fuel trims, transmission line pressure, shift points, etc., based on how heavy your right foot is. The transmission learns to shift according to your driving style with the old fluid, and when you flush it out and replace it all with brand new, It cant tell the difference. It still has all the shift points, shift times, line pressure, etc. stored in memory, but they are all based on readings using the old fluid. So before you condemn your tranny, try disconnecting the battery for a few minutes to reset the PCM's adaptive learn. I have seen many tranny's "fixed" after a flush by doing this. Of course it won't "fix" all of them, but if your tranny is acting up after a flush, it is worth a shot.
I'm not sure what year Adaptive learn was introduced, but I want to say 1997. I'm sure trannyman can fill in where I have missed.