Article on The Internet Mini Encyclopædia
The injection car has a return to the tank for fuel which is not used. My guess is that although the pump is drawing fuel from both tanks it is returning unused fuel to only one tank.
I've never worked on an injected mini so I can't tell you for sure where to find the return pipe, but when you do I suggest you put a Y piece splitter in it so returned fuel is sent to both tanks.
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