This seemed to have done the trick, I can use the mouse normaly now
As for the 2 display windows, I think I've read somwhere thats because the map was smaller than my screen, on other maps I don't have that problem.
Thank you very mutch for your help now I can play this game on my pc with the mouse, I have the first 2 C&C's on my playstation, and RTS with a controler sucks.