Hello. I have tried using the GECK in the past, and have some experience with the TESC from Oblivion, but I am stumped!

I made a vault, but was having trouble with my followers navigating it. To put it simply, they weren't.
So I thought I had figured out the navmesh system - plop down the 'points', select 3 of them in a rough triangle shape, then press 'A' and join them up.
I covered most of the floor in all the rooms this way (leaving out some of the tight corners which would have been fiddly and pointless), and now I have other problems.
When I entered the back door of my vault, my character froze. I don't mean the game, I mean my actual character! I couldn't move, interact with anything, even TCL (clipping mode) didn't let me move.
I entered the front door, and noticed my characters were in the ceiling. They dropped down after a few seconds, but definitely not good! I took a few steps into the room and my character froze again.

Have I done something wrong? I hope I can get some help with this as I am close to giving up.

http://img5.imageshack.us/img5/8453/navmesh.jpg

It seems to have something to do with the doorways - if I go near them my character freezes - stay away, and he's fine.
Edit: I removed a door, and my player could walk through fine with no freezing, but then when I moved further into the room he froze.
I deleted all the navmesh info and it's still doing it, so I am at a loss.

It definitely seems be a problem with the doors - I removed all but one, and had no problems until I approached this door, and got the freeze again.
The only thing I have done to the doors is make them 'Automatic', which I assumed meant they would close on their own. Now I'm not so sure...