You have the carbs with the vacum controlled fuel shut off valve on top of the carbs, don't you?
Could that valve be causing some touble with the fuel dlivery? Or dirt in one of the float valves, or T connections between the carbs, or even a partially clogged petcock filter? Also a partially clogged vent hole in the filler cap can cause this to happen.
Normally when you shut off the petcock and continiue to run a bike, or run out of fuel, all carbs won't run out of fuel at the same time. It will quit on one or two cylinders first, then on the others. If the fuel flow to the carbs isn't sufficient, I think the same thing can happen. You will have a fuel flow that can make it run on 2 or 3 cylinders, while one will cut out. With the 650 carbs that isn't unlikely, since the fuel hose from the fuel tank runs down between carb #1 and 2, and carb #3 and 4 are fed via carb 2.
I remember I had a issue with this once when the inline fuel filter I had put on started to clogg up with dirt. And it acted a bit like your bike. When the tank was full the gravity of the fuel in the tank would feed the carbs with out any problem, but when the tank level dropped to under 1/2 full, the partially clogged filter restricted the fuel flow enough to make it sputter on one cylinder.
It's just a thougt.