you need to adjust the rod as well, if its not adjusted your reducing the amount of fluid being moved
i have the same sort of issues with my brakes and from what I have gathered it just comes down to the master cylinder not having the capacity to push enough fluid through the system to apply enough pressure to all 4 wheels, when you pump it quickly your managing to force more fluid into lines, I want to sort mine out as well but never have found a definite solution, maybe a cnc master?