Elf Prince, I discovered what has been happening with NMM and it's wonky behaviour. Somehow (I have no idea how) another version installed in program files last December. Every time I try to update, it updates the hidden version. The link to NMM that I use on my desktop launches the version I expect to use, and if I click the download button on Nexus without NMM already launched, it launches the hidden version.
I'll see what happens when I delete the bogey version. If it fucks my Skyrim installs, I'll delete everything NMM and use something else. Mod managers shouldn't default install to program files, this is well known, and they should fucking update properly, not install a brand new version elsewhere. WTF?
If I understood correctly, you were updating NMM through the manager, right? I experienced problems few times (like many others) when doing it. So I rather download new version and ran installer.exe. It's much safer and it never freezes during the installation. It overwrites existing version and voila.
I assume that your link has some weird program in back up that starts unusual behaving. I always go the the Nexus and download the latest version. Then I check it with my Kaspersky antivirus and anti malware and anti spyware programs. When they confirm that the file is safe to install, I run th installer.
Before you delete your "bad version", copy your mod folder somewhere else because you don't want to lose them. it happened to me once or twice when I forgot to do it.