No brake pressure when engine is running?

[boostat4500]

I just got done doing an axle and brake swap ( 3/4 ton with rear disc ) on my 71' Burb. I've got the brakes bled and the pressure is good at the pedal. But when I start the motor it gets real mushy like it has air in it. No matter how much you pump the pedal it doesn't get any firmer. I'm almost 100% positive there's no air in the system. I had this exact thing happen on another truck about 5 years ago after it sat for about a month. I can't remember if it was the master cylinder or brake booster that went bad though. Any ideas? Thanks.