I have the same issue on my wr250x; it only happens when 1) I ride the bike for awhile, 2)its a really hot day, 3) and I'm at dead stop on idle. My bike is all stock except for the flapper being removed and I think the baffle on the stock exhaust has been removed.
I think there was a discussion about this on another thread just can't find it right now. I think I read from somebody here that it was a possibility that when you blip the throttle when the piston is at a certain location, it will stall. I don't know if this is true since I didn't remember much from that thread.
I just learn to live with it and made sure I rev slightly at a light so it doesn't stall when the light turns green to take off.
Sorry I couldn't help much.
I'll keep looking for that thread. If you end up finding it let me know.