Just curious....what type of proportioning valve are you running? Was it part of a kit that came with a master cylinder/booster? Was it a salvage component? Some prop valves have an internal pressure differential valve that has to be centered before you can bleed properly. Some have a little knob that you use a notched tool to pull out when bleeding.
I ran into the same problem when trying to bleed the system with a salvage m/c and (multi-line) valve....now I use the Wilwood Adjustable proportioning valve from Summit Racing ($39.00) on the rear circuit. It has an "in" and an "out" and I can regulate my rear brake bias as well as bleed without problems.
There is a lot of good brake info on the following sites:
http://www.ecihotrodbrakes.com http://www.mpbrakes.com http://classicperform.com Give us a little more info please.
Dave