I think I've found somewhat of an answer to the Door/Wall problem. Under Segments there is a short wall and a large wall. For some reason these two walls will not allow you to place doors and use them without the wall being there. If you use the segement like "Control Room Bottom" or another segment like this and select to paint the wall only, or pressing the F key, it allowes you to place the door and the wall is removed from the door area.
Still can't understand why the short wall or the large wall will not allow a door. What would these two walls be used for if you can't put a door in them.
Keep'em Movin