While not exactly problems, some graphic cards do not work well, or even at all in multi-user environments.
If you are building such a system from the beginning, check the Video Compatibility list before buying video hardware.
Sometimes secondary graphic card(s) (for now reported only by Nvidia owners) will refuse to start, even if they have worked flowlessly for months. One of the following sollutions should fix the problem:
Running /usr/X11R6/bin/X -probeonly on the secondary card(s) before initializing/ starting XFree on the primary graphic card.
/usr/X11R6/bin/X -probeonly -layout X2
/usr/X11R6/bin/X -probeonly -layout X1
/usr/X11R6/bin/X -probeonly -xf86config /etc/X11/XF86Config-4.X2
/usr/X11R6/bin/X -probeonly -xf86config /etc/X11/XF86Config-4.X1
Switching the secondary graphic card to primary, starting the system (to initialize the card as primary), and reverting the card to secondary.
In case this is the only secondary card, you can try switching the order of the graphic cards permanently.