Both Medal of Honor and Jedi Knight II use the Quake3 engine, so you'll have that problem with any Q3-engined game (such as Q3 itself, or Star Trek: Elite Force which by the way was made by the same team as Jedi Knight II, so if you see any similarities in the style it's not a conicidence).

For me, whenever I have refresh rate trouble, I just edit the system registry's refresh rates for that display and then use MultiRes to switch resolutions. I forget the key name, and it's not the same key in 98 as on my 2K box here, but I think it was somewhere in HKLM\System\CurrentControlSet\Services\Class\Display. You'll see multiple entries (0000, 0001, 0002) etc. for each video card that you've ever installed and it will have all the available resolutions.

I've had problems where certain games would try to run at 800x600x72hz on one of my old monitors that wouldn't do that resolution (it would only do 640 and 1024), and pounding on the registry took care of the problem.

I don't know if the DirectX video drivers are used in the Q3 engine for controlling the display refresh, but running DXSETUP will also let you force DirectX to a specific refresh rate.