I run a dual screen setup with 2 ATI Radeon cards (non Crossfire) and every time I run Unity I get the same problem.
I run the editor with both screens active (Extended desktop) I get a scrambled editor. (See image)
When I switch to single display it is fine again.
Can anyone tell me why this could be happening and if there is a way to fix it, short of running it single monitor?
That should not happen and is probably a graphics driver problem. Try updating your driver.
You might have an editor script in your project that messes up the GUI matrix or you use direct render functions at the wrong places. Try (temporally) removing your editor scripts or start a new empty project. If the problem persists It’s something wrong with your hardware / software configuration.
Keep in mind when you render something in OnGUI “manually” to only render it on Repaint event. Never do rendering on Layout or any other events.