Usually games use the default desktop refresh rate but there is a caveat. It's the refresh rate when the desktop is at the same resolution as the game.
Try this. Go into display manager and change the change the resolution followed but the refresh rate and save the settings. For example, if your normal desktop is 1024x768, change it to 800x600. (Almost forgot) change the color level to the appropriate one 16-bit or 32-bit, as well. Now, change the refresh rate to the one you prefer.
After you do this you can switch your display settings back to your preferred desktop because you have now established the default setting for other resolutions.
Any game that now uses 800x600 with the color level you chose should also now use the correct refresh rate. If it doesn't, then as someone else mentioned, the game is overiding the default Windows settings. You will have to manually set the setting you want in such a game.
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