Here is some food for thought....
I was talking to my friend today about the issue and he had mentioned the kickstand. Now I feel like he might be on to something.
It has only happened to me on a down shift and the kick stand is right below the peg....sooooo..
The scenario is: Down shift, possibly a hard down shift, it jossles the wiring or kickstand to the point the bike says "kickstand down, kill engine," even though the kickstand isn't really down. This seems to make a hell of a lot of sense to me.
I could understand if it was an idle problem and it was just dying at a light. But this is happening in motion and is most certainly not part of a break in period as it is a pretty big safety concern IMO. You should never have to worry about just dying mid intersection or on the road as a part of the bikes temperament during a break in.