It's definitely your cpu. When i got my GT for my old xp2400+ system, i got the same fps dips on the carrier and in training too as i did with my ti4200. Got an a64 which runs at only 200mhz more, i get massively better framerates on that level. Screen below is resized, i took it at 1600x1200 2xAA 8xAF, all the ingame options at VHigh water UHigh, but i didn't want to widen the thread with a huge image, so it's resized to 1024x.
Far cry really needs a good cpu for a steady framerate, it's the most cpu intensive game around, as far as i know.