My own viewpoint is that the existence of the Knossos provides the explanation. If one assumes that the Lucifer fleet in FS1 is the same fleet that destroyed the portion of the Ancient empire that corresponds to GTVA space as we know it, then one could easily see the Ancients shutting down the Gamma Draconis Knossos after they'd passed through, in a last-ditch effort to stem the tide. Unfortunately for them, the Lucifer was still essentially invincible, so they were wiped out regardless. The Lucifer fleet tried to return the way it had come, only to find the Knossos deactivated and their path blocked. Presumably, they then decided to either go into a state of hibernation until otherwise instructed, just hang out in the raw fabric of subspace, or do whatever it is that Shivans do in their downtime.
Fast-forward 8000 years or so, and all of a sudden, the Shivans start picking up subspace signatures all over the place, from two rather pesky species that seem to have a beef with each other. Maybe they decide that enough is enough after fourteen years of conflict, or maybe the GTI pokes its nose somewhere it shouldn't have, but either way, the Lucifer fleet finally wakes up and gets back in the business of annihilating entire species. As effective as they are at doing so, however, they're still using 8000-year-old ships. In the meantime, back in whatever mysterious regions of space beyond the Knossos portal they were occupying, the Shivans as a whole decided that the whole "beam cannon" thing they had implemented for the Lucifer was a pretty good idea, and set about sticking them on every capital ship in the fleet. Fast-forward a bit more to FS2, and these up-gunned Shivans pour through the newly-opened portal, only to find that there were two pesky alien species on the other side who'd figured out how to use the same sort of weaponry.
(Lousy post snipers.