The latest version of calibre,
literally released a few hours ago (what a coincidence

, calibre is released every Friday, about midnight Eastern Time, or Friday afternoon if you live in India), should have a fix for the malformed databases issue. The remaining libimobiledevice issue should be a Windows exclusive. See the post right above yours.
Make sure you have
calibre 2.10.0 installed, not 2.9.0 which was the latest this afternoon.
Report back, on the other thread, if you still have problems. But it should be fixed -- as you say you are on Mac OSX.