I was affected by this bug; but I am in a horrible location for Internet
and behind a proxy server. But I fixed my bug by deleting all of the
none default hidden folders in my root directory. I used gksu nautilus
in order to have the correct permissions. I then rebooted my machine.
Once I logged back in my machine was behaving normally again. Hope that
helps.

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Apt has strange network errors when updating indexes.
https://bugs.launchpad.net/bugs/574886
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