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From the symptoms you describe I would strongly suspect that it is your Firewall blocking Calibre. Any new install of Calibre is likely to be treated as a new program. Depending on what firewall software you are using this may require the Firewall to be updated to allow new versions to access the internet.
As Was early mentioned about the only other possibility is that there is a proxy setting somewhere that Calibre is picking up and trying to use. However you seemed pretty confident that this was not the case.
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