I have finally reached the point where I had to ask…
Every time I open Cubase (9.5.3), and subsequently scroll through media in the right zone, the media shown has been reset to show all media, even those in the folders I deselected in the last session. When I open MediaBay - surely enough - it has checked the same bunch of folders I deselected last time.
Interestingly, these are the “Cubase” folders, meaning “VST Sound”, “Factory Content”, and “User Content”. Is there any way I don’t have to uncheck these every time I open Cubase without otherwise using a sledgehammer?