I think it's the same problem as I see. Take a look at the bug report I opened last night -->
https://bugs.launchpad.net/calibre/+bug/1069617
Basically what I see is that the titles of books change; initially appearing with their original name, then changing to the name assigned via a metadata plugboard, and finally appearing with the original name. The "In library" column does not always reflect the true state either.