I have only come up with one idea. Check out my "Shift Time vs TPS vs Shift":
shift_time.PNG
My theory: The 0.75 setting allows the tranny to apply more pressure and get the 1->2 shift to happen when it takes too long. Meanwhile, the 6.38 second setting for 2->3 means the tranny waits too long to start applying extra pressure.
However, I don't feel confident enough in my own knowledge to change these fields, and furthermore if this was it, then there should be a much bigger difference between 1->2 and 2->3.
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