it sounds like the game is going to full screen and setting the resolutionand refresh rate. If the monitor make a click type noise then this is the case. To avoid it set the display option is the game to match your desktop resolution & refresh rate.
if you have an LCD its probably doing this to autoadjust to the new settings too but you won't get a click-like noise.
If your screen is constantly scrolling, change the refresh rate to something your monitor supports. ATI cards have an option in the catalyst drivers to force the display to what set for the desktop. You might try that too.
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