Sounds like a filter of some sort may have gotten flipped on. Are you sure there aren't any software control panels installed? Check all the players for filters, some players make changes to the system codec, so a change on one will affect all. Re-installation of chipset drivers(I'm assuming S3 is onboard) wouldn't hurt either.
Also, if you have another video card laying around, I suggest popping it in and trying it out. A screen cap of the problem would help too, it could tell us if it is a uniform change or just a random color change.