[WS64]

But Koreader searches for the metadatafile in the directory you specified. If you can search it did find one in mnt/onboard/.Books
But according to the way you exported the books from Calibre this file should be in mnt/onboard/ (and if you use this one all should work). But again that means that you manually must have copied the metadata file into the .books folder, are you sure you don#t have two copies of the file, one in mnt/sd and one in mnt/sd/.books?

Wait for the next nightly, this finally will have the defaults.lua editor, with that you can see (after one search at least!) which value Koreader found and uses now.

UPDATE: readeing your post again it sounds like Koreader took your value, did not find any metadata file in your directory, did an automatical search (but did not tell you, not sure why not!) and used the searched value. But again, you can see this with the next nightly by checking the defaults editor.
Actually I made things even easier, if you just leave the setting to the path to NIL (default value), Koreader will search for it. If you save the settings then everything is fine. But of course it will just find one, maybe I have to think of finding more than one Calibre file, e.g. one on sd and one on onboard. But then again someone could think of putting even more metadata files on the device...