Talvez o problema na ausência de bit SUID?
Aqui estão os arquivos que devem ter:
ip@ip:~$ ls -al /bin | grep rws
-rwsr-xr-x 1 root root 27256 2010-01-28 20:32 fusermount*
-rwsr-xr-x 1 root root 78096 2009-10-23 07:28 mount*
-rwsr-xr-x 1 root root 35600 2009-05-12 00:43 ping*
-rwsr-xr-x 1 root root 31368 2009-05-12 00:43 ping6*
-rwsr-xr-x 1 root root 36864 2009-07-31 16:59 su*
-rwsr-xr-x 1 root root 56616 2009-10-23 07:28 umount*
ip@ip:~$ ls -al /usr/bin | grep rws
-rwsr-xr-x 1 root root 14640 2009-05-12 00:43 arping*
-rwsr-sr-x 1 daemon daemon 52112 2009-09-16 01:29 at*
-rwsr-xr-x 1 root root 41864 2009-07-31 16:59 chfn*
-rwsr-xr-x 1 root root 37128 2009-07-31 16:59 chsh*
-rwsr-xr-x 1 root root 59752 2009-07-31 16:59 gpasswd*
-rwsr-xr-x 1 root lpadmin 14256 2010-03-02 17:16 lppasswd*
-rwsr-xr-x 1 root root 62368 2008-11-05 15:24 mtr*
-rwsr-xr-x 1 root root 32384 2009-07-31 16:59 newgrp*
-rwsr-xr-x 1 root root 42856 2009-07-31 16:59 passwd*
-rwsr-xr-x 1 root root 14880 2009-10-16 14:43 pkexec*
-rwsr-xr-x 2 root root 143736 2010-04-13 20:31 sudo*
-rwsr-xr-x 2 root root 143736 2010-04-13 20:31 sudoedit*
-rwsr-xr-x 1 root root 18848 2009-05-12 00:43 traceroute6.iputils*
-rwsr-sr-x 1 root root 10536 2009-11-10 12:48 X*
Tente definir a execução + SUID em todos eles (ou pelo menos no su) via
chmod u+xs file
UPD: note que para / usr / bin / at e / usr / bin / X você precisa fazer também
chmod g+xs