Using those files 3d was enabled in all the resolutions, but when I started a mission the screen stayed black and only the music playing. It locked up and I had to shut down.
Usually it only appears to lock up, it just takes a long time to load while showing a black screen.
Anyway I installed my GOG version of JK and had exactly the same problem with dgvoodoo until I went all the way back to 2.41. Now all resolutions were available but the game crashed every time I tried to load a level.
The solution was downloading the Steam fix from here:
(I only copied the exe, not JK.CD)
It works even with 2.44.
PS: Isn't Mysteries of the Sith supposed to be included? It didn't install with JK and there's only a download link for the Mac version in my library.
Edit: Refreshing my account fixed it. https://www.gog.com/user/refresh