I'll look at that code, though I'm probably not going to be much help for this. Note for these books it refuses to acknowledge any formats. They were originally put in the book directory by Calibre .5, so there's no issues with naming, etc there. Attempting to manually add a specific type of source file in the edit metadata dialog does nothing.
I'll go ahead and open a bug and attach my metadata.db.
edit:
bug is here:
http://calibre.kovidgoyal.net/ticket/3092