Just in case anyone else shares my situation... I use Thrive Architect, from ThriveThemes, for all my WordPress design work. Unfortunately, WP Media Folder doesn't work with TA. It doesn't "break" anything in TA, it's just that TA ignores the folder-structure I created in WP Media Folder. Instead, TA displays all images from all my folders in the Media Library - as if I had not created any folder structure. Very occasionally I create a page or post using the default WP editor, and WP Media Folder works great with that.
Very nice plugin; just doesn't happen to work with the design package I use.