Same issue for me. CTRL-Cing from checkinstall creates a /no-backup and
change the permissions of the root to /. See also
http://www.ubuntuforums.org/showthread.php?t=191477

Everything seems to be fixed by:
rm -rf /no-backup
chmod 755 /
as root, but this is still a major bug.

-- 
checkinstall hid my root partition 
https://launchpad.net/bugs/45763

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