Bike is stock ('98 so #48 pilot jets) except for Fuel exhausts with baffles in place.
I checked the fuel tap and filter, since this has been on my list of things to do since the bike is now at 59k miles. There is some what I could call scuffing in the edge of the diaphragm but it is not perforated as far as I can see and appears to operate correctly.
Carbs are perfectly synced and pilot screws are on 2 and 2 1/4 turns. I've tried them both half a turn in and half a turn out and it didn't affect this issue.
TPS is at 500 Ω.
I noticed that the rubber shroud for the front choke valve had come off the carb - I thought this could be the cause but putting it back has not cured it. Is it possible however that a fleck of crud has got sucked in to the choke valve during the time this shroud's been off? I think it will have been like that for a while, possibly since I changed the choke cable in December (since when I've done 10,000 miles

I plan to take the carbs off tonight and check they're all clean including the choke valves. I'll also check the spark plugs are tight (they've only got 6,000 miles on them) and will check the side stand and clutch switches and also the ECU connections.
Is there anything else which could cause this which I should check whilst I'm at it tonight?
P.S. it's not a carb fart - it does do them now and then but this is different.