This is a known bug in patch 2036.. what I will do is upload and post you the URL to the working mission script..
generally the install instructions for the 2036 patch are as follows..
Uninstall SFC EAW and delete the Taldren game folder.
Reinstall Starfleet Command II Empires at war, go into the directory of the game, fine the Starfleet2.exe, right click on it, select copy, go to your desktop, right clicik and select Paste Shortcut.. this fixes severa game bugs caused by launching the game from the SFC2.exe.
next go into the Assets\Scripts folder of SFC II and find Uni_7BattleGrave.scr and copy the file, paste a copy of the file outside the SFC game directory (remember this is a copy so do not remove it from the scripts folder)
Patch game with patch v2036.
Move the copy you created of Uni_7BattleGrave/scr back into the Assets Scripts folder and say Yes to overwrite.
launch game from desktop shortcut (always launch from this shortcut.. and in GameSpy Arcade, change the game option to launch from Starfleet2.exe) and enter your CD key.
Your game should play just fine now including the mission you are having difficulty with..
Now give me a few moments and I will get the script uploaded so you can download it and replace the one in your game directory.. This will help you prevent a reinstall of the game using the above directions.