Unless it's included in the next update, you may have to fix it yourself. Seems like it may be something to do with being an original DL scenario played through TA with the new races, but I didn't dig that far just looking for the problem and the fix.
Fixing it is pretty simple though. You pick the scenario editor from the TA launcher-editors. Now hit open and browse to C:\ProgramFiles\Stardock Games\GalCiv2\Twilight\Data\English\Campaign\Dreadlords and find look for the Apocalypse.gc2scenario. Note: Ultimate Edition's file structure is slightly different, but should be similar enough.
Note2:Once you have the scenario located, you might want to make a backup just in case the editor saves it weird or something.
Once you have it open you just go to the Win/Lose Events tab Where you will see "Defeat the Dreadlords" as the first entry. Select it and hit the edit button in the lower middle. You should see the problem as soon as the little window popsup. Under event parameters it says "If Krynn are eliminated then victory". Simply change that to Dreadlords in the drop down. Save it and hopefully your set to go.
I'm not sure if you'll be able to continue from a save within that map and get the desired effect or not. You may just have to play it out again.