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First, if you are unhappy with calibre companion (CC) we are happy to give you a refund. Simply send email from CC's about dialog to ask for it.
Regarding the message saying some other device is using calibre: this happens if calibre cannot "service" CC's connection in reasonable time. My guess is that you have something plugged into your laptop that calibre thinks might be a device, such as a phone being charged. It isn't necessary that whatever it is actually be a device for calibre to take time to look at it. If truly nothing is cabled to the laptop, including your nook, then we must look further. To repeat, to use a wireless connection nothing other than a mouse should be connected by cable to your laptop. In particular, your nook must not be connected via a cable.
Regarding the missing books: it isn't at all clear how you sent them given that CC apparently won't connect. CC can see only books sent via a wireless connection. As you say that calibre can see the books on the nook then it must be connected somehow, probably by cable, which as I said above will prevent CC from connecting wirelessly. If calibre is connected to the nook somehow, you can determine where books are on the nook from calibre's device view. Click on the book and then hover your mouse over the link in the book details window. You will see the path to the book on the nook. By default, CC stores books in the Calibre_Companion folder on the nook.
It would be helpful to know the version of calibre and CC you are running.
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