Do you have Windows Explorer set to show hidden files and folders? (
XP, Vista,
Win 7)
Maybe the graphics options file isn't created until after the game is started for the first time. I don't recall seeing anyone report it being in a different location for the Steam version, anyway.
If nobody with the Steam version replies about how to set the resolution, try emailing support@larian.com, with a description of the problem and maybe a link to this topic. You could also check the Steam forum, if you haven't done so already.