I'm neither a WoWI employee nor one of the devs, just a player who sometimes can help with problems — given enough information.
It sounds like you may have had some kind of files permissions problem, which I understand can happen with some versions of Windows (I'm on a Mac). Or perhaps, as you say, a firewall setting. I've occasionally had the WoW updater complain that I'm behind a firewall (which I am) but I've never had any problem with it other than the complaint itself.
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