Ok, you state that you are patched.. but did you follow the patching instructions correctly?
I will post all the instructions here in full. then I will tell you which to pick up from afterwards so tht you will not have to restart your campaign...
ALSO, make sure of patch version.. Interplay's Patches are over 2 years out of date.
SFC 2 EAW Patch Instructions :
1) Uninstall SFC 2 EAW using Add/Remove Programs in Windows Control Panel
2) Delete the Starfleet Command II directory off your system
3) Disable norton Anti-Virus or any other Anti-Virusfor the following steps, re-enable after done patching.
4) Install Starfleet Command II Empires at War from game CD, do not install Direct X or M-Player/Gamespy Arcade.
5) Make sure your Direct X version is Direct X 9.0b, if you installed a previous version of Direct X on top of 9.0b, it will corrupt Direct X and you will need to reinstall Direct X 9.0b
6) Go into your Starfleet Command II game directory and find the Starfleet2.exe, right click and select COPY, right click on your desktop and select Paste Shortcut.. Using this to launch game prevents several in game bugs from happening.
7) go back into your Starfleet Command II game directory, go into the Assets, go into the Scripts folder, copy Uni_7BattleGrave.scr and save it to a directroy outside Starfleet Command II
8) Depending on your game version (can be checked on your splash screen when launching the game) Download the correct patch for your region.
A) US :
http://www.nightsoft.net/effhq/files/SFC2Patch2002-2036.exeB) German :
http://www.nightsoft.net/effhq/files/SFC2Patch2102-2036.exeC) UK :
http://www.nightsoft.net/effhq/files/SFC2Patch2202-2036.exe9) get the Uni_7BattleGrave.scr you copies outside Starfleet Command II game folder and overwrite the one in the Starfleet Command II\Assets\Scripts folder.
10) Re-enable your Anti-Virus service
11) Launch game, enter CD key and have fun.
Now, since you patched while not following the instructions correctly, Here is what you need to do.
Go inso your Starfleet Command II game folder and go into the MetaAssets directory, copy the db folder and save it outside the Starfleet Command II game directory...
Follow the above patching instructions all the way through, then when done, copy your DB folder you saved outside the Starfleet Command II game directory and overwrite the one in your Starfleet Command II\MetaAssers directory.
Just remember that if your were not using the 2036 patch before now, that all saved games from different patch versions will not work and you will have to restart your campaigns. Example.. patch 2032 saved games will not work with patch 2036, the saved games will cause Starfleet Command II to crash. You will need to delete your saved games and start the campaigns over.
If you were patched to 2036 and wish to continue the campaign, then follow the instructions above.
Hope that this helps.