When it does this are you pulling away under load? Then it kind of hangs in a gear at high RPM and then finally shift? A bad throttle position sensor can cause this. Or does it seem to slip as it shifts? For that you may want to have teh trans oil pressure tested.
Hang on a second, did you say this is a new transmission? Because what your saying sounds to me like the gearing is wrong between the transmission and the tune. An example is if your old transmission has 2.93 gears, and the new transmission has 3.29 gears that will throw off the shifts.