Problem with programs requiring root

[bloch at verdurin.com]

I'm running Breezy on a laptop that used to run Fedora, so I kept the
/home directory.

There's a strange problem with the installation in that it appears none
of the GUI programs requireing root authorisation work properly (e.g.
Synaptic, the software update tool).  When I try to run them, nothing
happens i.e. in the case of synaptic or the update tool, I'm asked for a
password, that appears to be accepted, but no window appears.

Any ideas as to what's going wrong here?