Are you using a pump flow controller? If you are then I'm thinking it might confuse the hell out of the controller. The way I see it is that the water will always take the easiest route, same as electric going to earth. The path of least resistance.
I can see it working without a controller although again you'll have a problem if one pole is higher than the other.
I'll be interested to hear the solution

Possibly put an in line flow valve on the shorter pole to balance the pressure between the two poles.