It could be the position of the pump in the system I guess... Maybe the normal pump 'sucks' from the side of the engine with the header tank on, and pushes it through the engine. If your pump is trying to push it through the engine from that side, it would be increasing the pressure towards the header tank too.
I'm not sure I believe that though, as the header tank is pressurised - it shouldn't really matter what the pump is doing...
In all our old cars we used to have a lemonade bottle tied in somewhere, with the water overflow outlet from the header tank going into it. I think when the engine cooled down, the lack of pressure inside caused it to pull the water back into the system, so there was never any problem...
