Andy with your switching around of the tanks, is it possible that air is leaking in now round the tap? The other thing is, the good fuel is in both tanks in case there is some switching anomoly. I'm not sure whether you have an early model with a turn tap or pull out tap.
(I had a problem on a pig that drove me mad for ages the fuel gauge measured the fuel in the tank you were not using. The Army upgraded my prototype to the pruduction plumbing arrangement but didn't changeover the wiring!)