I don't know if this is a CK issue or not, but when I went to wrap up my mod testing for the night I noticed I had 3 interior cells missing. They were completely gone for the cell list! Is this a CK issue or is someone fiddling with my computer when I'm not around?

You may need to elaborate... If they are gone that means that you either didn't save, or you didn't load your file or something like that.

Last I was modding everything was working fine, everything was where it should've been and all that. I load up my CK today and do some modding to add a new interior cell, I didn't even load up the cells that have disappeared. I go to run through my entire mod in-game when I'm done and notice that a house is turned sideways in Riverwood, 2 interior cells were completely deleted and one interior cell is still there but completely empty. I have no idea how that could have happened.