Could always be a carbon fouled plug.

Ok so i never got a definitive cause for this problem. We had a winter blast (snow, flooding etc) so i did valve clearances, There were a few (7!!!!) on the tight side but none offensively and all on the inlet side iirc. had to buy 5 new shims due to them mostly being wrong in the same direction and similar sizes anyway. However upon start up bike runs fine and ive never had it run on 3 again it also idles much nicer. So i guess that this did sort it ... or maybe it was the extended dry out time for the plugs. (in saying that, swapping the plugs for known good ones never helped)

I also bought a tyga bolt on can (wow LOUD :) ) and it turns out that it is a lot freer flowing than i thought, having to go up to 112s then 115s all round and still maybe thinking its sliiightly too lean when doing a plug chop, Those little brass bastards aint cheap

Hope this helps you as it can be a real mind F**k at times eh. I spent many hours in the garage scratchin my head.

Oh yeah if you do your valve clearances DONT forget to put some rags down the holes... I spent near on 1/2 an hour searching for a (my 1st!) shim after it slid off the grease and i realised i hadnt put rags down in my haste to get started... when i found it under a rocker arm there was a bit of this going on I felt dizzy with relief coz thats a big scary hole down the camgears! Rags down the holes at all points from then on!

Just remember to take the rags out when you finish. Otherwise they end up in the sump and block your oil pump destroying your engine.

I had this problem today
Started bike on stand and it was only firing on 3 cylinders, no. 4 (front right) was not firing.
Turns out, for me, it was fuel related. ie, not enough in tank, even when on reserve.
Topped up with jerry can and fired up first time, all 4 running
No problem