I've actually been having a similar problem, although I only get the juddering sometimes (mostly on training missions for the FS2 campaign, although it happens rarely in the story missions as well). Turning the framerate indicator on shows I'm still getting a solid 60 FPS. The problem goes away when I turn Vsync off, although of course I get tearing when I do.
I just downloaded and installed the game a couple days ago, and I'm running the FSO 3.6.10 build and the media VPs, including that advanced one. My computer isn't quite as much of a powerhouse as WDeranged's is but it's still respectable, running winXP pro on an 8800GT and an athlon X2 with 2 GB of RAM.
I haven't tried the detailed troubleshooting that WDeranged has done yet, mostly because my problem doesn't seem to be as annoying as his, but I'll do that when I have time. I just wanted to let you guys know that it's not an isolated incident.
EDIT: I should mention that the juddering doesn't seem to start until I target something, and stops when I'm not targeting anything.