I have the exact same problem with my "Balmora House Mod". I've been looking for a permanent solution for some time, and it will probably involved editing the save file using the TESAME program. However, there is a *temporary* solution. What you can do is open the console, and left click once on the door. The door's name/ID should appear as the title of the console. Type in "disable" and the door will dissapear. Once you reload the game however, the door will re-appear. Disabling BOTH doors will mean that one of the doors will re-appear in the next game, and then two will re-appear in the next. Frustrating, no?
