Now NMM has only 2 active mods: Skyrim, and update. It still has all my mods as checked active. I know this immediately because I am going through the wagon ride (new game) instead of starting with a “new start.” I exit Skyrim, and look at NMM. Then I go into the game, and it looks like none of the mods are active.
I then download like 30 other mods, and do the same thing. When I do, the mod shows up in the “mod” tab with a check mark next to it. I have watched the youtube video that tells me to click on a downloaded mod, and hit the “activate” button. I am using the automatic mod manager to make things easy.