All due to water in the petrol.

Quick check:
After engine has run for a couple of minutes open the filler and look at the petrol. If its cloudy (or in my case looks like bad milk) you've got watered petrol.

Cure:
Let the water settle overnight, put the bike on its sidestand and siphon using a clear 8mm tube into a jamjar with a metal top. Try to get the end of the tube right under the strainer of the fuel pump.

I got about a pint of water out and some interesting lumps of grot. No problems since.

I was lucky enough to work this out quickly but siphoning the tank is now on my yearly service list

A cup full of Methylated spirits will do the job well and it seeks out every molecule of water and takes it through the system as the mixture will be suspended in the petrol.

Just in case no one else mentions it, Gerry.
How did it get in to the tank in the first place?
The favourite is that the filler cap is on the tank the wrong way around and allows water that has collected there to fall into the tank when you open it, instead of draining away through the vent.
The cap should open towards you rather than away from you.
Many of us have been there. 
You shouldn't need to siphon the tank. Could be worth removing the fuel pump and cleaning the pump well properly.
Takes minutes to do.

Thanks RickG, I will do that.

Comberjohn:
As near as I can tell the water all came from a single petrol fill from a garage in Harlow I don't normally use (and won't again!).

Petrol cap seals, vents and cups are all fine. The old bus has stood out in some pretty torrential storms and I've not had a problem.

I did pump fuel out of the high pressure line into the jar until it was mostly petrol before turning to the siphon. I now think it makes more sense to siphon first then run the pump.

There's still a little cloudiness in the tank after the engine has been running but I hope the meths will zap that. I had been thinking about installing a fuel drain, a la light aircraft, but it would be difficult to get to.