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Based on what you have told us, there are at least four things that could be causing the problem: a router that is failing, your Nook, your computer, or calibre (and that might be related to the version. You need to try and isolate as many of the possible causes as possible in hopes of narrowing down the problem (my guess is the process of loading books onto your Nook is responsible, not calibre itself, but it certainly wouldn't be the first time I was wrong about something).
First, you list your device as a Sony. Did you have this problem with the Sony or did it start with the Nook?
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