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I had an empty partition at my drive and decided to clone my system to that partition.
Well, I just copied entire the root filesystem (excluding tmp, proc, sys and dev directories content), tweaked grub.cfg, /etc/fstab and rebooted into freshly cloned system.
All seems OK except one thing: I can't run su, kdesu and sudo commands. In fact I can do it, but I getting "Authentication failed" message when I entering root password. It occurs both in GUI and CLI.
However, if I (being switched into CLI with Alt+Ctrl+F1) logging in as root directly (without su) I can log into root account.
HOW did you copy that root file system? If you did a true clone, it should work. If you did a COPY (cp) then certain ACL bits would not transfer and this behavior is exactly what you should expect.
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