the marks could be a residue left from a cleaning process, or lack of cleaning. if the board is coated it could be the coating starting to peel, or the coating scratched by a previous installation, or the coating reacting to a cleaining agent.
none of which would indicate a failed motherboard. however, if its water staining you should clean it up.
you could try a non-silicone contact/electronics cleaner, you can get it at an electronics store, and clean it off with a lint-free cloth.