Morrowind plugins keep getting disabled and reordered

[Maarsz]

Hello, recently Vortex has started disabling a few Morrowind plugins (seemingly not related to specific .esp) and changing the load order at random at each deploy, Morrowind uses file dates for load ordering, so maybe the issue lies there.
I've also noticed that often (but not always) those plugins then show up as "Not managed by Vortex" in the load order tab, even though they come from mods installed through Vortex.

I'm on vortex 1.13.3, using GOG Morrowind GotY, and have never had this issue before over the years up until recent update/updates.

[Pickysaurus]

Try using the "Purge Mods" button to temporarily remove all of the files Vortex controls, then check the plugins list. If it includes things that aren't part of the base game, they've somehow got into the folder without Vortex controlling them. Try deleting any extra files and then deploy your mods again. 

[Maarsz]

2 hours ago, Pickysaurus said:

Try using the "Purge Mods" button to temporarily remove all of the files Vortex controls, then check the plugins list. If it includes things that aren't part of the base game, they've somehow got into the folder without Vortex controlling them. Try deleting any extra files and then deploy your mods again. 

Nope, they are still marked as Not managed, and again after enabling all plugins and deploying a second time, the "random disabling of plugins" still happens, both on plugins that are marked and those that aren't.
It doesn't seem to follow a logic as to which plugins get disabled and which are kept enabled.

I also checked if Morrowind.ini was read-only, which it isn't.

[showler]

Are you using OpenMW by any chance?

[Maarsz]

32 minutes ago, showler said:

Are you using OpenMW by any chance?

No, plain ol Morrowind on GOG.

[Maarsz]

Reinstalling the marked mods keeps them marked, BUT they don't seem to be disabling anymore.
The only ones that do are the Merged Objects & Merged Lands plugins, which, being two plugins that are (re)generated with TES3Merge & Merged Lands respectively, can't be managed by Vortex.

EDIT: It might've actually been fixed for good with the latest Vortex update.