I don't know much about Windows systems (that warning message doesn't look like any Mac OS window I have ever seen) but basically CS3 is considered quite old and may not be compatible with certain processors regardless of the number of cores. I'm afraid that computer technology never stands still and everything becomes 'old' very quickly.
Have you tried checking if this issue has been discussed on the Adobe Help forum and if not, ask the question there. Adobe techies unofficially post there and can help - I know this because that's how I got head-hunted for InDesign pre-release development.
