Alright, I too have had a faction turn into independents, my own. Basically, here I was with three dominators two lashers and a hound trying to defend my three pirate stations against the combined alliance of gedune, council, and lotus. The station defence fleets were completely wiped out, the council were everywhere with their particularly powerful ships, and I was assassinating boarding ships (in-system station attack fleets) in order to keep my stations alive. We had just ended up at peace with the lotus conglomerate when the white background of death reared its ugly head, and I saved my game, restarted starsector, and re-loaded. I don't actually know when the change from pirates to independents was made, nor even if it was before or after the save since I had already made a later save by the time i realized that I was no longer a pirate, but by the time I had finally fought off the other enemy ships and boarders until peace once again reigned in the system, I looked at my fleets and stations and realized that I was independent.
Hopefully the in-depth story will help you to find the bug.
Also, I noticed that once the stations and fleets in the system get up to full power, it is near-impossible for fleets of other allegiances to get a foot-hold past all of the defense fleets when the new arrivals are immediately beset upon by an alliance of three. I noticed a poor antediluvian fleet arrive in the system to be attacked by that triple-threat, and the only thing that remained of them after just a couple in-game days was a fully armed antediluvian capital ship taking part in the attack of my own stations, having been captured by an already large council fleet. I suspect that the fleets such as this are going to need a bit of an increase in power before they are able to really affect much.
Also, I would love for there to be an option for even more than the current number of planets and stations available, even if it does result in a bit of overlapping.
Edit: Oh, and one more thing, the regular attack fleets, while sent out in a time of war, will continue to fly around the opposing stations long after a peace has been reached.