Hello Modcraft, this will be a short tutorial on how to fix WMO's in Noggit 1.3, in the event that you are experiencing npc's falling through the floor in your server, or just being stupid in your WMO's.
This is a picture of a skeleton, who'm is under the floor

This chapel was saved in Noggit 1.2, and I extracted the maps and he fell through the floor.
This is because for some reason 1.2 doesn't save WMO's properly according to Steff, so in order to fix this you have to re-save the WMO in Noggit 1.3, then re-extract the maps for your server.
Make sure you understand that, to re-save a WMO you don't just save the terrain around, you have to actually move it in Noggit 1.3, or replace it.. Whatever you wish, as long as it gets edited.

This ^ is the chapel before I moved it in 1.3 after being saved in 1.2, as you can see there is no green bounding box which I think represents it's pathing some how. Maybe someone can tell me what the green box is. But, if it's not there, when you extract the maps, your WMO will be broken.

I middle clicked the WMO, and it has correctly shown the box.
Now when you save, the WMO will work in your server after your re-extract the vmaps and mmaps and place them in your server files.
Hope this tutorial is helpful to those experiencing problems with WMOs in their server. Goodbye!