It could be the extra timing. Advanced timing will cool the internal pipe temperature down. There may be some residual effects from the midrange timing advance once you get to peak rpm. It should go away in fairly short order. If it is not going away quickly, you had better check your peak timing with a timing light and make sure both boxes are the same at their peak. Even a degree or two advanced will make a difference. If you find a difference in peak timing on the two boxes, you can most likely adjust your stator to compensate depending on the engine you are running.
Good Luck,
-Starting Line Products, Inc.