I had a very similar issue when touring in Lake District a couple of years ago and it turned out to be the sidestand switch.Any slight bump in the road would cut out the bike.I'd get off put it on the sidestand and it would, obviously, start straight away.Try putting the stand down next time it cuts out and see what happens.
You're definitely on the money Dudeness - I went out for a test run, with a bit of wire wedged in the SS ground on the ECU so I could probe it, died within 200yds, no ground. Engine starts up right away if I short the pin to ground, and then dies again when I remove the short.After a while it decided to work again, and then died for a while after I dropped the seat back down. Wiggling the wiring around the rear of the tail doesn't seem to have any effect. The immobiliser still makes all its usual beeps and things when it won't start - so its power, ground and switched ignition are still good.Considering it cut out when I placed the seat down, and it wasn't moving, I'm inclined to believe the fault may be in the immobiliser rather than the ignition switch - some kind of transistor-y thing breaking down, as it allows a small amount of current to go to ground when the bike is off. Any better ideas before I make a mess of the immobiliser harness to bypass it... and still have the problem?