Hi Verooie,
can you please try this :
right click on the desktop shortcut for SS Extremes, go to properties > compatibiliy
and check "disable visual themes" and "disable desktop composition" (something like this, depending on your Windows Language).
Click on OK, and start the game again. Your Anti Aliasing settings (if they're enable in your ATI video drivers settings, if not you might check this tutorial : http://80.95.161.114/shipsim/forum/index.php/topic,19579.0.html) should be back.
PS : this applies to windows 7, maybe vista too.