Flicker can be related to AC frequency in your country (50 Hz in Europe).
http://en.wikipedia.org/wiki/Mains_powe ... _the_worldMost electrical lamps do produce flicker because of use of alternating current. When you record video at the same frames per second (50 fps) as your lighting flicker frequency (50 Hz) it effectively "masks" the flicker.
Paradoxically, sometimes your motion capture results can be better when you do have visible flicker on video. The problem is that you still do have flicker when you record at the same FPS as your AC frequency (because usually it is
not exactly the same) , it's just less visible for a human eye because it is low frequency. Visible flicker can be considered a high-frequency noise, and it can be easier to filter out then low-frequency noise (using the Jitter Removal filter).
I recommend that you do test captures in your environment at different frames per second and compare the results to choose the best FPS setting.
Now about video cards.
The 8800 GTS is actually not that much inferior. We do not optimize specifically for NVIDIA cards, but various NVIDIA and ATI/AMD cards can have different performance trade-offs and can behave differently in iPiStudio. I can tell for sure that latest top NVIDIA cards (GeForce 560 and 580) are seriously faster in iPiStudio then latest top AMD/ATI cards. Older generations should have more similar performance.
The difference in speed can also be caused by different CPUs in your computers.