It is possible the QuickLook cache believes that the thumbnails are up-to-date and does not call Camera RawX to generate a new thumbnail, but provides the thumbnail from the cache instead. If you see thumbnails being generated in a new folder, but generic thumbnails are presented in an existing folder, you will need to clear the QuickLook cache.
Open the Terminal app, and type the following:
qlmanage -r
qlmanage -r cache
Then reboot your Mac so Finder regenerates the thumbnails. On recent versions of macOS, restarting Finder alone is no longer enough — a full reboot is required.
Fixed in Camera RawX 2.4.0. Update from the Mac App Store and X3F thumbnails will render correctly, even with Sigma Photo Pro installed.
If you were previously affected, you may also need to clear the QuickLook cache (see section 2 above) so Finder regenerates the thumbnails.