For some reason,"save media cache files next to original when possible" had come unchecked in my preferences.
That is default setting and for a good reason. Now you have cache files scattered across different folders: some of them will still be located in default Media Cache Files folder, while others in folders where your media files used in a working project are located, and if you want to use Dynamic Link, cache files for the replaced clip will be duplicated in a folder, where AE project file is located.
Probably a better solution is to clean Media Cache Database manually, i.e. delete all files from both Media Cache and Media Cache Files folders, and let PrPro rebuild it from scratch. Such cleaning will also free up some disk space.
Meanwhile, if you have some delay in Windows Explorer response outside PrPro, you need to test your hardware.