My 2005 X does the same when it's warm despite having the better ECU and a brand new TPS, new filter, good plug and correct idle speed (1500 when hot) (all stock apart from MTC cans). Happened to me a couple of times yesterday in traffic - I have a tendency to blip the throttle. Have also had the engine cut when blipping to downshift. I think it might just be a trait of it being a big single, although it wouldn't surprise me if it's related to the bikes being lean, in which case maybe a Kev mod would fix it.