NMM says all mods are deactivated?

[rchood13]

Recently I updated NMM (I also had to renistall steam and my game and installed FOMM to fix a problem so that may contribute.) and it doesn't seem to recognize that mods are installed. All the files have red x's as if they are not installed, however they are and show up in my load order. The only way for a mod to be deactivated is to uncheck it or delete its files in the data folder, which is too complicated. When i select a mod in the manager it can be activated and it overwrites files, but when i deactivate the mod does not disappear from the load order and goes back to how it was before. I'm not that good with mods so it's probably something stupid, but i can't figure it out. If i could receive help that'd incredibly swell!