Okay, I think I've got a related problem. Noticed it before installing the source project, and it has persisted after the installation of the source project + upgrades.
Namely: The central HUD options are off-center by about 1/4 of the screen.
The friendly and enemy shield indicators, the HUD hull/shield indicator, the weapon energy/afterburner indicators, the escort monitors, and more likely than not the missile lock-on arrows are all off-center. The only one I'm able to see is the HUD hull/shield indicator, which is halfway on the screen, down where the enemy ship profile would be shown. The rest of the on-screen indicators are fine, or at least seem to be, although no box popped up around the comm menu.
I just recieved the game today, and installed the source upgrades.. but like I said, I saw this before said upgrades were made.
I am running WinXP SP2, an ATI 9600xt card, 1 GB Ram, DX 9.0c December 2005 update, Omega Drivers 6.1 revision, and the P4/XP/64 version of the source upgrade.