Is there a way to improve performance of Flip3D using two monitors?
With a single monitor it feels a lot smoother.
What graphics card do you have and how much memory does it have?
Flip 3D will require more memory and processing power than normal windows and when you double the area it has to operate across you are increasing those demands still further.
Also - while you might get good 3D performance when a windows is wholly contained on either monitor you might find a performance hit if it spans both. This is because the processing can't be done by one output path alone.
The ultimate solution might be that you have to buy a more powerful graphics card - or just live with the degraded performance.