To the best of my knowledge, it has been like this since after the initial install. I've been using the command line to install, then thought I would use synaptic, to look up a package or two, and that is when I noticed.
So you have been using apt-get from the command line? In a terminal try:
and see if you can use synaptic after entering your user password.
I did not change the default, for the root password during installation. The su-to-root command, root's password doesn't change anything.
In a terminal can you change to the root user? In case you have never done it, in a terminal -
then the root password when prompted.
My guess is that the root password is not set or not registering. You can try changing it from the command line, and then try running synaptic again with su-to-root.