The screen flickering is a known issue I believe, but it was supposed to be fixed in most of the recent driver packages. It had to do with the idle clocks going too low when a 2nd monitor was attached.
As for the change in FPS... could be from having 2 monitors plugged in. In fact it might be the same issue. If the idle clocks are having trouble, maybe in 3D it clocks up to the wrong speeds. Normally there's idle, UVD, and 3D clock settings. For my 5850 they are 157/300, 500/900 and 700/1000 (stock, mine's actually 870/1200).
So... what drivers are you using? You could definitely do a complete reinstallation with 11.4 and see if that helps. This would include completely uninstalling the drivers first, rebooting, running driver sweeper to get rid of everything, then rebooting again and installing.