I've put up an experimental version that should address the issues with adding the books to calibre after a build. If anyone is feeling lucky, please give it a shot. I've not added it to the update feed, you'll need to install it manually from the following link.
Install Link
I've tested this under Windows and Linux, but don't have access to a Mac. It should work, but you never know.
One big change, your calibre path on the Mac should point to your bundle directory, something like /path/to/calibre.app. This is for Mac only, under Linux and Windows point to calibre.exe.
If this seems to work, I'll spend some time adding more logging and error checking and do a real release.