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The door to the Census and Excise Office from the inside courtyard to where the captain is is missing. One can understand how problematic this is at char gen. Anyone know what mod could be causing it?

Missing doors are often a symptom of a localref conflict problem. Most of these kinds of problems should be fixed by the Morrowind Code Patch (MCP), so it would help to know if you are using it. If you aren't, that would be the first thing I'd try.

If you are, then it may be a rare case that it doesn't catch, in which case finding mods that modify the cell "Seyda Neen" (-2, -9), and using Wrye Mash to "renumber refs" for those plugins might fix the problem.

Once upon a time I lost the door to Gravius' office, too. I could never track it down, but two things stand out. One was that in games in which the door was missing, there was always a potion of levitation behind the barrel that contains Fargoth's ring. The second is that after the most recent MCP was released, it has never happened again.

Once upon a time, my hold it mod hid this door inside the wall, that was the very first release of hold it and was fixed within a week. (there was no potion of levitation though)
If you have the very first release then http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=7474&comment_page=1 is the culprit. The later versions are all free of this problem. They also come with a series of addons including for Children of Morrowind which you are using.