I'm also having problems with my flash lagging/stuttering, but only when it enters full-screen; normal-mode it's fine.
I'm running 2 monitors, NVIDIA 560ti; it happens on both monitors.
I also have the problem that if I put the flash full-screen on my second monitor, clicking anywhere on my first monitor will take the flash player out of fullscreen.
This doesn't happen with my Chrome 38.0.2125.104, only the Opera Dev 26.0.1655.0 that I have; so I have to switch to Chrome to watch anything fullscreen.