I like the reed idea for sure, that could be inconsistent.
I had a newer 150sx do something very similar, it would just all of a sudden spike into the powerband when you were feathering the clutch.
I actually attributed it to the powervalve and sure enough, with a little bit of tweaking on the preload screws, it was better. The 250 doesn't use the same design, but still its an interesting thought.
Ohh and NO, I have never had transmission issues with the KTM's. I've ridden quite a few, they've all been spot on. Remember, new bikes are kinda strange, it takes a while for things to wear in and I wouldn't doubt a bit of abuse and your dog ends will wear a tiny bit and you'll be all set.