Not the smoothest transition, is it?
Yes, after 2.04 there is 2.20, which is essentially the Community Update database with a few bug fixes from Stardock, all wrapped up in a full-game release. It changes only Twilight; the others are unchanged.
Are your latest Dread Lord (original) and Dark Avatar chapters in the same base directory as Twilight? (E.g. in Program Files\Stardock\GalCiv ?)
In the meantime, play Twilight 2.04. It's a step up from the older stuff all by itself.