Did you bench bleed the mater cylinder before installing it?  There could be air trapped in it.

The master cylinder could be defective (not unheard of).

Did you flush the brakes lines of all fluid and replace it with fresh?

Did you bleed the lines in the proper order?  Right rear/left rear/right front/left front...any other order can leave air in the lines.

Did you mix DOT 5 synthetic fluid with DOT 3 or 4 non-synthetic?  That is a definite no-no as the two types are absolutely not compatible.  You will get lots of air bubbles that will not bleed out and create a soft peddle or worse.

Did you rebuild the calipers?  In my own case, a '78 Vette I owned had a bad caliper seal that was sucking air in, not leaking fluid out.  It took a while to find that and it led to lots of soft pedal issues and once the pedal went to the floor but I barely had enough to bring the car down slowly and have it towed on a flatbed to a shop.

Have the rubber hoses ever been replaced?  Just because they look good on the outside doesn't mean they haven't gone soft internally.  If you can't verify when or if the hoses have ever been replaced, it would be a good idea to replace them all for safety's sake.

There could be a few more possibilities...hopefully someone can mention them.