I have the same problems after installing a new graphics card. However, this is no showstopper and I won't shell out any money or time to get them fixed
1) After starting the game, the LucasArts logo (accompanied by the IndyTheme music) and afterwards the Collective logo (also accompanied by some sound) should appear. Both don't appear anymore, however, the music is played.
-> I used to skip them with the ESC key anyway, so this does not matter to me at all.
2) The Loading Chapter graphics don't appear anymore. The screen is black at that point.
-> Loading a chapter takes some seconds only (average is around 5 seconds on my machine), so I don't care about that very much.
-> BUT: This also affects the PlaneFlyingToNextLocation animations, such as when you have finished the Prague chapters and now move to Istanbul. This is not so nice, as I would like to see these animations. However, it doesn't depress me so I can comfortably live with it
3) The cut-scenes, however, are *not* affected! To make it clear: The cut-scenes happen within a chapter to point out important things, they are animations within the gameplay, and these cut-scenes work well. If they wouldn't, I would consider this a showstopper, but they work.
Just my .02