I have had this issue before and I fixed it by editing something in the Ini file (I think) but I can not for the life of me remember what. But it basically makes the Creation kit load every single thing in that's listed in the object window. (Apparently the ini file is set up to only load partials, and not even let you load more then one master file without editing it I have already had to edit the damn thing about 4 times just to get it to allow me to make more complicated mods, its stupid and ridiculous and all of this [censored] should be enable on it by "Default").
If anyone knows how to set it to do load everything, please let me know.
Thanks