your problems with X may be derived from gdm (gnome display manager)
have you recently tried installing a different window manager other than gnome, like KDE or Fluxbox? These managers also provide a layer of session handling for users, if you attempted to install an alternative, a config may have gotten chumped...
what i would do in this case, is boot into a debian/debian-like live CD to make your changes, so that your actual filesystem stays intact until you can discern where the problems are, using fsck to check your drives from a live CD may also be a bit slower, however it will allow for a better check as the HDD's dont have to supply the rules.
does your installation have alternatives you can choose from in Grub?
What exactly were you doing when the problem displayed itself to you? Your best bet would be to retrace your steps and let us know what was going on, this will help us to troubleshoot the problem with you more efficiently