Are you using the script to convert, or trying to do it manually?
Included in the download is a file called DOE_NW7SpecialFleetAssault.scr and it should be in your DOEConvert folder. When you run the ToDOE script, it places three copies of this file in your Assets/Scripts folder and names them x1, x2, and x3. These three copies appear in the mct file, and are thus supposed to make it much more likely that you get this special fleet action when you attack an enemy base. The missions is very nasty, and is keyed to appear only over bases.
For the record, this doesn't seem to be working. The missions showed up fine when I was only running it and a base assault for testing, but now that I've expanded the mct file to the full 49 missions all I ever seem to get on a base is the base assault and the Evil Dave base assault. <shrug>
Still, if you are trying to install manually, you'll need to make three copies of DOE_NW7SpecialFleetAssault.scr and place all three in your assets/scripts file.
-Herr Burt