I've also been hearing word that NMM may be some malicious software, which the creator himself might have to check with, or if it is intentional. Either case I recommend you use caution when you use third-party programs like NMM. I stick with the launcher, either that or I still use OBMM, and FOMM for instance. Just a heads up for those who wish to protect their computer, because I for one will not use it at anytime in the future, or ever.
Seeing that I don't use NMM to activate my mods on the games I play, I don't really know the program well enough to troubleshoot or assist you further with this issue. Though I wish you luck in fixing it though.
EDIT : This is why.
_________________
"Some men just want to watch the world burn." -Alfred Pennyworth**Screenshot story-arcs on hiatus until further notice**