[hharney]

While looking at the attached fuel system schematic, it looks like the most likely culprit would be the selector valve. I don't think the check valves would be a suspect. One set of check valves on the return lines from the fuel pump/throttle body and the other check valves are on the vent for the main tanks. Are the bypass valves, near the aux fuel pumps, check valves?

To have fuel transfer from one main to the other would almost have to go through the selector valve but if the bypass valve is one way only it would have to pass through this also.

I would inspect the fuel that you have in the tanks to be sure that you are not taking on H2O as Rodger has described. Either leaky fuel caps or corroded service bay drains can allow water into the tank. Plug the bottom of the service bay drain and allow some fuel to spill over into the service bay to be sure the tube is not compromised.

From reading your scenario it sounds like the fuel transferred but it is best to make sure.

Cheers mate