Skyrim won't let me change reorder load order

[NiftyPower]

I recently ran into another bug where Steam seemed to think that Skyrim wasn't already installed, even though it was. So I went through the reinstallation procedure (after copying my settings files, such as SkyrimPrefs, etc. to restore after the installation process), and after restoring my settings files, I was able to play Skyrim again.

 

However, when I try to change the load order using the Skyrim mod organizer, I can move the mods around in the organizer, but no change is saved. And when I open the NMM, I can't move any mod up or down. However, if I manually change the load order files, I can change the load order. So why can't the official Skyrim mod organizer or NMM reorganize my mod list order?

[Valkyrie]

You might actually have Skyrim installed in 2 different places on your pc. Check your settings on NMM to make sure it knows where your latest installation is. You can also use LOOT to sort your load order for you: https://www.nexusmods.com/skyrimspecialedition/mods/1918/

[NiftyPower]

That doesn't seem to be the issue here, from what I can tell. I managed to get the Data Files load order sorter to work, as far as I can tell. However, when I load NMM, it changes the load order to what it was set to a while back, and does not let me change any files.

This is for all mods, existing and ones I try installing now, and mod dependencies have nothing to do with it.

If I uninstall and reinstall a mod in NMM, that becomes the new position for that mod in the load order, and THAT new load order overrides the load order I set up in the Skyrim Data Files mod load order.

[NiftyPower]

I think I've partially figured out the issue. In the folder Users\<user name>\AppData\Local\Skyrim, there are two files that store load order, loadorder.txt and plugins.txt. The default Skyrim load order sorter changes plugins.txt, but not loadorder.txt, and when NMM loads, it overwrites plugins.txt with the load order from loadorder.txt. However, if loadorder.txt and its backups are deleted, loadorder.txt is created from plugins.txt when NMM is opened, and the load order determined by plugins.txt is preserved.

 

Since I never bothered to check this before I had an issue with this, is this usual behavior? I'm trying to figure out why NMM can't change the load order, since it used to be able to.