is the top clone choppy when its not the active window, but gets better when active?

hit ctrl-r .. see the frames/sec ... if you set your maxfpsbk to something low, it could look choppy.

if you haven't, maybe you should. pushing over 60fps while in the background is a waste of cpu, gpu, system and graphics bus

try it and tell me what happens.

as an fyi.. good to compare your card to others:
http://www23.tomshardware.com/graphics_2007.html