[Talung]

I have figured out the problem.

Thanks for your help Kovid and others. I have figured out what my problem is. Essentially I believe it because I am modifying books on the Linux system and then rsyncing to the Windows system where I in turn modify them some more and rsync back. Somewhere along the line certain folder names get changed in Case.

eg.
Piers Anthony/Chaining The Lady (742)
Piers Anthony/Chaining the Lady (742)

The case of 'the' got changed. The books reside in the the uppercase one but the metadata points to the lowercase one. This means in the web intereface it shows the formats as being present, but in the application as not being present. This also explains why the "not format:epub etc." command returns them as being there even though the application says they are not.

Gonna be a bit tricky to find, but I think a troll through the folder list and look for duplicate numbers in '()' should reveal any folders that have been duplicated. Then its a manual application fix to change the book name to point to the correct folder.

Thanks
Tal

BTW, in case anybody is interested. To find the folders that are not unique but contain the same calibre index number in brackets I am using this bash command line:
$ find -iname "*(*)" | awk '{print $NF}' | sort | uniq -cd