Yeah, just checked, and whenever I close GECK and reload the mod like 50% of the room I had placed previously is deleted...weird.
EDIT: Yeah, I checked it and while I found the roombounds hiding the Brotherhood bunker, I can't find any on my bunker I'm working on. They are the big blue boxes, correct?
Yes thats waht roombounds look like.
You bring up that view/ show/hide window. There's a checkbox for seeing roombounds. Make sure GECK is in a mode where it can see into your cell and see if they are there or not.
Assuming this isn't roombound problem: When you load your cell, look into that cell browser window thingie which shows all of the items, in a text-like form, which are in your cell. Try double clicking on some of them from that list. The thing you are searching for is, are the items there in the render window but just invisible, or are you really, totally missing 50% of the stuff?