This performance issue can occur with newer GFX-Cards, supporting OpenGl 4.0 and newer, its is most common on Windows Vista and Windows 7.
How to fix:
Renaming the EF2.exe into quake3.exe
will solve that issue. Since EF2 is based on the quake3 engine and is using the same or a simular OpenGl version the GFX-Card driver will handle the game correctly when it thinks that it is quake3.
Elite Force II it self has not yet been added to that driver exception list by ATI.
If that alone doesn't help also try the following command with the ingame console: com_maxfps 85
You have to rename the executable file exactly, to quake3.exe, it should not be named quake3.exe.exe. If you only read the name "EF2" at your Elite Force II executable, then rename the file to "quake3" only. If you have it done correctly, then the renamed executable should still show the Star Trek Elite Force II Badge icon.
For more informations
please read the originating thread