So, I recently went back to dig up an old mod I'd worked on, in the GECK (I switch between it and FO3Edit), what I found was I couldn't set it as an active file. After a moment of confusion I noticed that the mod was showing up as a master file in the GECK. FO3Edit and the files extention both confirm that it's an ESP.

I also noticed there's a lot of files in the GECK's load list that are no longer installed. I have the impression that these two things are somehow related, but I'm not sure.