Downgrading to nVidia drivers v 260.99 fixed this problem for me. When head ani's play, the game no longer goes choppy.
I'm running into these same issues, cept I'm using a three (maybe four) year old laptop. Geforce 8600GT.
Also running the final build (3.6.12) MediaVP's fresh from Turey's Freespace installer, running the standard FS2 campaign. Also occurs in the FSPort. (Downloaded yesterday, so most current versions available to the fsoinstaller)
Installed fresh last night, ran Turey's installer, downloaded "the works" and everyting appears to be in order in the install dir.
I thought I'd fire it up and check out some of the new campaigns, and I'm running into the choppy/hitching sensation, and it occurs in fullscreen mode, only when a head animation plays back in the window. Disabled mouse and ran only keyboard. Seems to only occur when running in Fullscreen or Fullscreen window, but in windowed mode it's smooth as silk. Native res I'm running at is 1440X900
I'm going to downgrade to 260.99 and try that to see if it will stop the choppyness. Also tried latest nightly build for Windows, SSE2 build, and I'm running into another odd problem. In addition to the chop, the hud jumps around while turning. Occurs only in fullscreen though. Windowed mode everything stays still.
I've forced my processor to run as fast as it can go, and not throttle down. No difference.
Has/had anyone had any luck on this problem?