This happened when I fitted my new doors. Mine was quite bad and I couldn't shut the door at all really without putting my knee through the door skin trying. I had to bend the lip which the seal sits on inwards away from the door to give room for the seal.
If you take the seal off and sit inside, you'll should have about a 10mm gap all the way round between the door and the seal lip. On mine it was just the front edge of the seal lip which was too close. I got abit of sill edge trim to protect the lip, clamped mole grips onto it and bent it inwards bit by bit.
My car has also just been resprayed and with bending the lip, the paint around the bottom of the lip will crack, theres no way of avoiding it. You could try heating the lip to soften the paint before bending but I doubt it'll do much. I just repainted my lip with a brush afterwards, afterall its under the seal and a pretty hidden area anyway.
Edited by mike., 02 September 2010 - 11:07 AM.