The lower crossover pipe is quite large, so a blockage would be highly unlikely unless someone has been stuffing socks into your fuel tank. There is also a high mounted air transfer hose to allow air movement between the tanks, and if this is kinked or blocked fuel won't flow between tanks.
Also, M3Ws are sensitive to the method of fueling. If you try to fill at too high of a rate the pump will shut off before the tanks are anywhere close to full.
Ideally you should be fueling from the left side of the vehicle (gives a more favorable angle for the pump nozzle) and you should fill either at a slow rate (preferred), OR, when the pump clicks off, wait a minute or so (to allow the transfer tube to do it's work) then pump again.
And as noted above, you cannot rely on your fuel gauge, so are you sure your tanks are near empty when you are trying to fill them? These machines really need another type of sending unit.
