I have faced the problem on the same system with dual booting. When I shifted from Linux to Windows or vice versa I had to auto adjust so that screen borders were recognized correctly. Resolution was the same, 1024x768 on both OSes.
In Linux, install system-config-display if not already there so that you get file
/etc/X11/xorg.conf or you can also use command (as root)
Xorg -configure :1
to create a new configuration file in
/root. See what the values are for
VertRefresh, etc. in this newly created file. If there is nothing then you can specify things manually so that they are same as that on Windows. Use
to see what all you can configure in 'Monitor' section in
You would have to find what the values are for these parameters in Windows. Look for some tool or maybe a graphics card driver that can tell you this information.