What I did was just searched in the C:Program FilesUbisoftSplinter Cell Pandora Tomorrow directory for *.ini and perused all of them for anything that looked like resolutions. Replaced everything I came across with 1680x1050, set Read Only atrib and as in your case too, it still defaults to 640x480. I wonder if they did this because of the online mode and not wanting cheaters (widescreen isn't cheating, it's an advantage! :))
So so far I can only get 1280x1024 which sucks. I think someone is going to have to come out with an exe hack because I have a feeling Ubi put some logic in the code that says "IF res is set outside 640x480, 800x600, 1024x768 or 1280x1024 THEN default to 640x480"...
I wonder...
How do you load the game? Do you use that menu that is fixed at 800x600, or do you go straight to the Single Player or Multiplayer executable? Will the .exe's work without coming from the loader?
Could it be the loader program that's stopping the widescreen res?
Try setting up a link straight to the single player .exe, and write protecting the splintercell2.ini so that it can't be changed.
I'm just guessing, but it might be worth a shot. :)