[Jac Mac]

There will be two recovery ports in your dual master cyl- one for the rear & one for the front portions, you might have the freeboard reduced to the point where one never opens & therefore maintains residual pressure in that part, preventing proper bleeding of the system, I have also seen examples where rebuilt M/C have had the divider seal ( not the correct name, but it keeps the fluid from front & rear sections seperate ) on the rear piston( Front in cyl ) fitted back to front which effectively turns the whole system into one rather than dual.. Try the car on some smooth wet concrete from about 20 mph in a panic stop & have observers check all wheels for braking ( Exercise caution while checking).

Is the motor modified, the booster seldom functions as designed once manifold vac is altered