With the exception of a mechanical problem, it could just be that you dont know what to expect after break-in. The bikes temperment changes a lot, it revs low and seems to have pretty good power at low rpms until its broken in and then its just screaming top-end. Make sure you're running 50:1 or close to it, running too rich can make it rev weird and lose power in certain areas. Also, if you havent already, change the plugs, that makes a big difference since in the beginning you're supposed to run a little rich for break-in and the plugs foul up fast.