Since it works to use the command line, I suggest that you run a set of commands to make sure your system is updated correctly. Well we know it is not, but this way it may be improved. The tips come from oldfred, one of the most experienced helpers at the Ubuntu Forums.
You can use sudo in front of each command or do as described: sudo -i first ... and exit afterwards (to return to normal privileges)
Edit: But since guest is OK, there might be something wrong with the settings of your user id. Can you remember doing something, that might cause the trouble (something else than updating the program packages)?
# This will reinstall if not current. (from my chroot procedure which does not have sudo on every line,
# so use the sudo -i first).
#if not chroot use: sudo -i
apt-get autoclean # only removes files that cannot be downloaded anymore (obsolete)
apt-get update #resync package index
apt-get upgrade #newest versions of all packages, update must be run first
#would upgrade you to the latest kernel in the repositories
#dist-upgrade is also able to remove existing packages if required
# fix Broken packages -f
sudo apt-get -f install
dpkg --configure -a