Do the files have accurate embedded tags? Was Plex previously configured to prefer local metadata? If the answer to both questions is “Yes,” it may be that you haven’t configured Plex to prefer embedded tags this time.
If your tags are very accurate, Plex will do a pretty good job organizing your files, even if the folder/filename structure isn’t what Plex recommends. If you’re not using embedded tags, then Plex has to depend on the folder/filenames to identify them, and having all the files from multiple albums in a single folder won’t work.
