EF doesn't modify the original CoH so your problem probably didn't start with EF but the other way around.
If you have this problem, it means your graphic card doesn't support your Company of Heroes current graphics settings. Make sure you hve installed the Direct X routines package, update your video card drivers and try different shader settings in the Graphic tab on Options.
If you try to run CoH using an Intel video chipset as replacement of video card it is probably the reason it is not displayed correctly. And probably there are not anything to do, because these are not made to run this kind of games.