I got the same issue as the guy on http://www.tomshardware.co.uk/answers/id-1763491/extremely-low-fps-monitor.html
his solutionFor some reason when I open up a game in full screen mode, my second monitor when showing my desktop will get a massive amount of delay and will get below 1 FPS.
I run games via Steam and changing compatibility mode to windows 7 on main Steam application does not solve the problem.I finally figured it out, it's a windows 8 issue! If you have Windows 8 and you're experiencing these issues, just run the fullscreen application in Windows 7 compatibility mode.