None of my skyrim mods show up only the Expansions and Skyrim.esm shows up. Yes, I installed all the mods in the correct folders, etc. Also for Fallout New Vegas it shows the mods and I check them but when I go in the game they aren't working. I quit and check mod manager again and none are check. It's not saving the checked mods and it's not even showing the mods for skyrim. Any fix for this? It happened once before and fixed itself but it's not doing that now.

What version of NMM are you running?

I would also suggest posting on http://forums.nexusmods.com/index.php?/forum/406-nexus-mod-manager-open-beta/

0.55.1 and I have tried posting there before they weren't very helpful.

Did you recently update or change the version you are running?

I just recently installed it since this is a fresh install of windows

I fixed my issue by downloading the 0.60 alpha which is funny since that version is in testing and the stable one is causing more issues.