That actually explains a lot, I used to run a lot of factions along with IX during the Arsenal Expansion days and really the only time they got wiped out was when I decided to go all out on them, to be honest most of their defenses back in the old version are not too difficult, in fact whenever I needed a pristine nanoforge I usually visit them to teach them a lesson about sat bombing so many worlds. I turned on Brawl Mode after they lost their first colony to Diable, hoping that at least they will spawn more defensive fleets to counter the invasions, I didn't realize it will only exacerbate things.
And if possible maybe make them play a more active role when it comes to launching invasions, because I swear before they are conquer planets at a faster rate than even the Legio or the Hivers.
One thing I realized that custom fleet spawns just doesn't even seem to work in 0.96 anymore, 3 times I saw Mariaath getting occupied by the Heggies even though the Vengeance of Mariaath fleet is still clearly active. I think maybe it's just that invasion fleets now make a beeline for the target planet now instead of the defensive fleets in the way.