Ok.. some people leave out information about the EXE files..
for Starfleet Command II Empires at War, you need to make a desktop short cut to the Starfleet2.exe game file.. to do this, go into your Taldren\Starfleet Command II game directory and find the Starfleet2.exe game file, right click and select Copy, go to your desktop and go to an empty spot, right click, and select "Paste Shortcut"
for Orion Pirates you would do the same thing only the file is StarfleetOP.exe and it is located in Taldren Software Inc\Starfleet Command Orion Pirates
the problem with running the game off the SFC2.exe or SFCOP.exe is that these files are bugged and they will cause the keyboard to malfunction, missle loads to work incorrectly, improper reporting of mission results, etc..
that is why it is important to use the proper file to launch the game..