My guess is that AMD software wants the top left corner of the main display to be at (0,0) but I wanted it at (0,40). I assume AMD overwrote my settings in the registry for the main display only, bringing it back to position (0,0).
Thanks for suggestion, I have not been able to figure out a preset though. I cannot even get AMD to acknowledge the custom positioning, let alone program it as a preset. If I trick windows into accepting it (I can change the registry entry and then "switch user"), as soon as I touch AMD or any program that uses the video card (even my browser apparently) the display positions get reset. I cannot see how I can set up the custom position with AMD ccc. CCC has a that drag and drop desktop arranging screen but it uses some sort of snap-to grid where the displays always seem to get aligned along the top. The Windows "screen resolution" menu at least lets me align along the bottom but AMD does not. Is there somewhere in the AMD software where I can set my monitor positions manually?
edit: It is definitely CCC, for now I disabled at startup in msconfig and problem solved! I assume as soon as I start that program it will overwrite my settings again. I don't even know what I would use CCC for. Am I missing out? I know the nvidia program was bascially useless except for scanning for games and suggesting graphics settings.