Many monitors have boxes that usually only pop up for a few seconds (or when they change modes) that generally tell you the monitor is not set to its optimum resolution or refresh rate. Usually the recommended settings are the highest the monitor can handle with a 60Hz refresh rate on LCDs. Have you tried just using the recommended settings?
Never used a monitor at anything other than it's maximum/native resolution. So that would explain why I've never seen this.
Good to know for future reference though.