This is speculation, but I've seen it happen before on laptop hardware. Your video drivers are incorrectly reporting the hardware's proper dimensions to the X server.
I've only, personally witnessed this on Nvidia video cards using the OEM Nvidia drivers, and with a Toshiba Satellite 6100 model laptop. The problem there was that it was giving back a slightly smaller number than actual, so I had a quater-inch wide strip on the right hand side of the screen that would not display anything when using X.
To me, it sounds like a similar issue.
I would recommend reviewing your x.org config files and checking the message boards on the manufacturer's site of your video card as a starting point.
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