So it turns out Windows has locked Stagsi DLLs in Program Files which prevented thumbnails for GIFs (and other files) to work. I can’t really pin point the cause for this because it doesn’t repeat all the time.
If you face a similar problem again, open Properties of any DLL in Program Files\Stagsi\Plugins and see if it says “Unlock” on the bottom. Or just remove the entire Stagsi folder and install it again (don’t install without removing the folder, the locked state seems to persist unless you remove the file).