If none of the GUI applications work, you could edit your /etc/X11/xorg.conf to include explicit DisplaySize, like this:
Option "CalcAlgorithm" "UseFrameBufferTiming"
DisplaySize 432 324
DisplaySize is the size of your screen in mm. It can be calculated by multiplying your native screen resolution with the dotpitch of your monitor. In the above example: 1600x1200 and .255 dotpitch >
1600x0.255=432 and 1200x0.255=324. This isn't required in most cases, though.
Of course, it may also be a video driver issue. I have noticed before that all my screens come out wrong (too much to the right) until I install the proprietary nvidia or ATI drivers rather than the open-source ones.
You should also be able to resize your screen by using the buttons on your monitor.