I seem to have found the solution. I just go back to C:ProgramDataUbisoftTom Clancy's Splinter Cell Chaos Theory and edit the .ini files then check off read-only in properties. Read-only protects the files from being switched back to its default on launch.
1280x680 ? Typo or HDTV ? :P
Maybe you fiddled with the wrong files... Try reinstalling then only edit the files that are in C:ProgramDataUbisoftTom Clancy's Splinter Cell Chaos Theory
HDTV...yea its a weird resolution I know. I had problems with my 1280x720 res after I installed a update for Windows 7. So I set a custom resolution in Nvidia control panel.
EDIT: I accidently clicked "create a topic" instead of "create a reply" the first time I wrote this down. Mods, ignore the topic I created.