Like I said, the shift points in the TCM tune are a goal for where the WOT shifts are supposed to happen. If the truck with 350hp come up at 400rpm per second and the trans learns how to "time" the shifts to get them to happen at 3250, then you tune the truck to 500hp and it comes up at 500rpm per second you just threw off the TCM's "timing" on the shifts. The command for the shift starts at the same time as it was before but since the RPM is coming up faster it gets to a higher RPM before the shift actually occurs. Think of a batter that always plays against guys that throw 80mph fast balls, he gets in front of a guy that throws 100mph and he is gonna swing late. Get it now?
On top of that as Shane said if you ECm tuning was done to fix your speedometer for tire size it can throw off the shifts.