First, in a multi site it is better not to use the network activate because the plugin has to scan each site’s media library data an that could take a long time which would be too much for the server to handle. It is better to activate the plugin on each individual site.
Second, you need to try a Media Library Folders database reset on the site in the multi site that is not working. This clears the folder data the plugin previously collected and then does a fresh scan of the Media Library As described in the Support section of the plugin, under Troubleshooting Tips,
Folder Tree Not Loading
Users who report this issue can usually fix it by running the Media Library Folders Reset plugin that comes with Media Library Folders.
1. First make sure you have installed the latest version of Media Library Folders.
2. Deactivate Media Library Folders and activate Media Library Folders Reset and run the Reset Database option from the Media Library Folders Reset sub menu in the dashboard.
3. After that, reactivate Media Library Folders. It will do a fresh scan of your media library database and no changes will be made to the files or folders on your site.
