EDIT: I fixed it. After I re-installed Skyrim, I also had to re-install SKSE, and then when I tried to use NMM again(after re-installing it), I was getting an error in-game telling me that SKSE wasn't found, so I ended up having to run skse_loader.exe as administrator to get it to work(then I set it to always run as admin in properties), so then I tried to use Mod Organizer again after fixing it, and now it works. The only downside is that Mod Organizer prompts you if you want to open it every time.
