Just so we can get to the bottom of it and know how to detect/workaround in the future.... Like Chris said, there are 2 programs: OrbiterGen which takes the large, high-res source graphics, and does 'pre-rendering', scaling and drawing text and building the actual pre-rendered for the Orbiter in folder /usr/pluto/orbiter/C[orbiter device]. And then Orbiter itself, which either runs on linux, windows or Symbian via Bluetooth, using the pre-scaled graphics.
It sounds like originally they assumed the problem was Orbiter, but later suspected OrbiterGen. You mentioned the fix with your video card... But I don't see how that could effect OrbiterGen, since OrbiterGen doesn't use the video card at all--it renders everything in memory and just writes png's. On the other hand, while the Savage3D could affect the on-screen orbiter in your core/hybrid, it couldn't affect the other orbiters too.
I'm really confused. The Savage3D shouldn't break OrbiterGen, nor break any Orbiter other than the one running on it. When it was broken, do you know if the generated files in /usr/pluto/orbiter/Cxxx where correct, so we narrow it down to OrbiterGen or Orbiter?