Ok, thanks for the link. I'll keep that in mind for future reference. And it looks like it's happening for both file types. I tried installing Cinematech, GNR Enhanced and a couple of patches for FWE for Fallout 3 and NMM says they are installed (by showing an install date), not showing a green check mark and sometimes giving me the selected plugin has been manually removed pop up. If I close and reopen NMM, none of the mods are showing as installed at all. Thanks for the help by the way!
EDIT: So it looks like it definitely is not activating any mod with an esp or esm but texture mods (I think) are working. I installed a High Res weapon texture replacer and that one is showing the green check mark with an install date but I haven't checked it in game yet.
Edited by Th3Dude, 16 January 2015 - 02:24 AM.