So, I'm a good 20 or so solar years into my first betrayal playthrough, and I've hit a bug which is going to soon make me lose the game! Here's what happened, from memory.
1. I invaded the acturian homeworld and managed to subjugate them.
2. The Evucs, Burlusts and Thoraxians all start warring with me.
3. The Evucs aren't technically at war with me, have a positive disposition towards me, but are constantly sending ships to attack me (but that's another story).
4. The big one. When any non-thoraxian ships are in orbit around my planets, I can defend against them, but the thoraxians come up as being neutral during the battle. If the ships are all just thoraxian ships, then entering the battle to defend my planet causes my ship to instantly disappear and the game claim that I am victorious. Upon leaving the battle screen, they are still there, happily tearing away at my defensive armadas, as they do, y'know, being thoraxians and all. I don't mind that they are difficult to beat, all adds to the challenge, but I can literally do nothing but watch as my planets get ripped from me. I can't afford to replenish my armadas fast enough, neither can I afford planetary ion cannons. In the time it would take me to build them, my planet would be lost. I'll keep the save file where it is, maybe you guys want it, I dunno.