Fluid pushing back into the master is normal. Do you have drum brakes on the rear? The reason I ask is that drum brakes move a lot more fluid each stroke of the pedal, the return springs force the fluid to move back. Discs only return a small amount of fluid and it can be gradual so maybe you couldn't see it. Have someone pry a caliper back while you watch inside the master, I'm sure you'll see it - especially if they do it to hard/fast! But more important to me is that verifies the push rod isn't applying pressure to the master and it has fully returned!
Another thought occurred to me when reading your reply.. You said you tested the booster. HOW? Also, did you bench bleed the new master cylinder? And I mean on the bench, probably clamped into a vise and you could observe the fluid / air moving through the cylinders??? Another thought I have is this a whole new car with all new parts? Or is this an old car that you're bringing back? reason I am asking that is there were some through the frame bulkhead fittings that had a differing size and they would actually trap air in the system.