Auto Config should (in theory) reposition the viewing area of the screen dependant on the resolution.
So it fires up when the resolution your monitor is working at is different than the native one (1280x1024), if it's working in windows - set the resolution to 1280x1024 and it should work ok.
right click on desktop>properties>settings
p.s. also set the refresh rate to 60 hertz.
Or possibly a buggy graphics driver,uninstall the driver and install the latest driver or even roll back the driver.