Did the disc brakes come from a donor vehicle or did you buy a kit? If you are using an emergency brake, could the cable be hanging up on anything, does it release completely? I'm assuming they bled normally, could there be any kinks in the lines?
I've seen something similar when the pushrod was adjusted too long and there was a preload on the MC, but shouldn't happen unless you made some changes. Did you change anything else like the MC, proportioning valve, booster, pedal or pushrod?
You may want to try loosening the 2 nuts and see if the MC pushes away from the booster with any force. If there is no preload, you should be able to hold it flush against the booster with very light hand pressure.