I aggree with Skeet, When I replaced the door seals on my PV444, I took the doors off. That was the only way I could get the seal inside the front channel. I used yellow 3M trim cement. Over the years I found that this bonds much better than the black. I clean the channel and the rubber good with either enamal reducer or laqure thinner first, apply some glue stick the two together, pull them apart so they get tackey then set them for a final set. Works great. I tried putting the seal on with the door on and it just would not stay in causing the door to not close (like you are discribing) Mark the hindges before removing the door. (unbolt the door from the hindge and not the hindge from the body) have someone give you a hand holding the door on re assembly and it will be easier.
Good luck,
Dennis

I can't give you a certain answer, but will ask"did you install the seals with the doors off the car. I installed mine that way and then was able to make very small adjustments to make the doors close properly. My GUESS is that the seal is either installed with the wrong side to the body, or that it is not in the channel on the front side of the door. Hope this helps.