Thanks.
Right; that's what it did with the previous versions, but this time it is creating playlists from some of (about 100) the album folders. I've just looked and yes, there are some M3U playlist files, but they weren't there before and I don't know how the hell that happened. Would simply be a matter of deleting them and things should return to normal?
EDIT: Since writing the above, I have deleted all M3U playlist files and rescanned my folders and the playlists are still in Musicbee as well as some new ones!