Ah. I removed everything and dragged it all back in, including the thm files. I used linking (see below), and voila all the thumbnails are there now. Yay. Thanks for that suggestion.
I am definitely using linking, not copy. I do not want to have copies. I'm planning to use jAlbum for thousands of images and pdfs and videos, so I read up on copy, link, mirror and decided linking is what I want to use. What do you mean by dodgy? Seems like there are bugs

Should I do some more experimenting and submit a bug report?