You shouldn't be running as root anyway. Don't log in and out. Debian uses sudo, to run a program such as Synaptic Package Manger or similar, just do a:
After which you will need to give your password, not the root password. If it says you are not in the sudoers file, do the following:
you@hostname$ su #enter root password
#scroll to bottom, add the following line to the end:
yourusername ALL = (ALL) ALL
then log out, and in again.
If sudo complains again, restart your computer (shouldn't have to). Its better to use that than running as root.