I have a 90 F-150 that does the same thing...... i believe what is happening is when you are running on one tank, when it returns fuel, the tank switch valve is not working correctly and is actually returning the fuel to both tanks,...... If it is only using fuel out of one tank, any time the key is on, you are circulating fuel, at some point the fuel will then all be pumped into the tank you are not using.....
Make any sense ?
I just never felt like replacing the 350.00 (from ford) switch valve in the frame.