This is a post I just made in the Calibre forum. Putting it here just FYI, as I think the issue is with Calibre, not CC.
When I sync from Calibre to Kindle via USB, I sometimes later eject it (windows 7) to allow it to charge. If I then try to sync my Nexus 7 using Calibre Companion, it fails saying Calibre is already connected to another device. I have to pull the USB completely to overcome this.
Is there a Calibre setting I've missed that would solve this, or...?