When you install Windows 7 the old fashioned way, the resolution of the desktop is automatically set to the native resolution of the screen. However during my LTI deployment I noticed that it was still set to 1024 x 768 which annoyed me to no end. After a quick look in the default MDT unattend.xml I found the solution.
If a resolution is set in the unattend.xml (<deploymentshare>\Control\100), Windows will force itself to use that resolution. If nothing is set in the unattend.xml Windows will set the native resolution of the screen. Therefore the solution is to remove the display sections in the unattend.xml. These lines should be removed: