First off, I thought this was actually a joke post, so that one was my bad and I'm sorry.
When you get it back from the dealer, let us know what they said. I'd like to know if the transmission just broke or there was another problem I've never heard of anything like this happening before.
ALWAYS break in a new engine component. Any part of the engine be it piston, entire top end, crank, conrod, or all of the above be absolutely certain to break it in properly before riding it hard.
I just broke in a piston like this:
start up for the first time, let the engine warm to the touch with just little blips of the throttle. do NOT overrev it.
Ride around gently for 10 minutes using 50-60% of the rev range. Let it cool off COMPLETELY.
Warm up the engine to the touch, again just little blips don't over rev it. Ride it around gently using 60-80% of the rev range. Let it cool off completely and repeat this one again.
Thats my warmup and the one time I've used it it worked well. I checked with both my honda manual and googled around a little. Like chump said the newer bikes it shouldn't be as bigger disaster. You should definitely still do it but it won't be the end of the world if you don't do it properly.
Again though, post up what the blokes at KTM said happened cos I'm interested.