Is there crud in the peg hole? Or maybe the distributor shaft and lower shaft fit too tightly to each other. They should be a snug slip fit. I've had to take a stoke or two with a file on some repro shafts so they slipped together.
If the head and/or block have been shaved too much the shafts might be holding the distributor up. You can feel the up and down freeplay of the distributor shaft as you try to push the distributor down to seat the peg. I've never had one not seat all the way. Make sure the head hole and distributor shaft are clean and rust free for a good fit and good ground. Antiseize is good to use in the hole so the distributor doesn't get rusted into place.