Is there a way to increase the refresh rate? I have FS2Open installed and I'm playing it with the MediaVPS mod. When the game starts it is at 60Hz and I do not currently have any external app that locks the refresh rate. Is there a command line or something to set it in the game?

Since your question is about FSO, you'd be a lot more likely to get a (fast) response at Hard Light Productons, since the code wizards reside there, among other people.
I glanced at the command-line reference in the FreeSpace Wiki, but nothing caught my eye regarding this matter.

Do you not have the control center utility for your video card installed? I'm not too sure about Intel's, but both the ATI and Nvidia control centers allow you to force the refresh rate of your choice.