Running Powerpoint (2003) slides through SM to project on the secondary monitor had the slides sitting mostly offscreen. The layer that Powerpoint was on was working for images and powerpoint run by itself was able to display on the correct screen.
It looked as if the sldes were the correct size for the second screen but displaying on the first screen with the extra spilling onto the correct screen, except that there was nothing on the primary monitor (laptop screen).
When I tried using the 'Primary 50%' setting a similar thing happened with the bottom left corner of the slide showing in the top right of the SM live display area. Live monitor correctly shows what the slides look like.