If you open the doors dialog box (Screen -> Doors) and hit "OK", whatever door type is shown in the boxes will overwrite whatever is already on the screen. Quite annoying for when you already have custom/manual doors set up. In my case, the north door is lock blocks, the east door is combos (to look like a doorway), the south door has no door combos on it but is rather a passageway, the west door is a wall.
I hope this makes sense, I'm not sure if I explained it well enough >.O