FOUND THE PROBLEM!
schlumpf originally found the answer to this problem http://www.mmowned.com/forums/model-...ls-noggit.html but he didnt explain it properly. First add your.WMO into the .ADT via the Noggit command line tools then go into Noggit and do as following
1. Select the .WMO you want to save
2. Press the "k" key to save
3. Go to the next .WMO you want to save and repeat 1-2
You must do this to every .WMO you want in order for it to stay.
Hope this helps, it did for me :P