I meant *I* wanted to continue with your game. Which I did last night, and I confirmed that the issue is fixed.
I also fixed a bunch of other stuff, namely some of what you just reported: colonies will not rebel for the next 2 turns (they shouldn't have been able to rebel in the same turn, but there was a bug), and the AtWar status will be resumed (their Regard towards you should not have been so high, will have to investigate why...).
[BTW, "building" an Unrest Order will prevent rebellions while it is in effect]
I also added a couple more restrictions for rebellions, they were not making much sense: they can only trigger if population > 2 * garrison, and if there is no station in the sector.
I guess I could add a modifier to the rebellion roll based on any owned combat ships in orbit
One thing I need to add is a SitRep when the civ is completely subjugated (but not necessarily eliminated).
Your savegame was really helpful
I tried it in Mar31 build and it almost worked but after first turn all the fog of war disappeared = I could see all the stars localization in the galaxy, but of course without any details.
Weird. Savegames are not compatible because of some changes to bonuses I made. I still need to make some more changes in that department...
I also tweaked bombardment damage: was decreased for garrisons and increased for civilian population.
I'm currently adding a Trade Route income decay with distance; it was kind of silly IMO to have a TR crossing an entire quadrant netting you full income. Now there's a max "length" for a TR to have no decay, and beyond that length the income decays at a rate of 10% per sector in excess. A closer but less populated system might actually be more lucrative. I will have to show that in the Economic overview mode of the starmap though, will do something similar to ship range.
Max length increases with your Propulsion tech level - there was discussion about making it useful outside of combat the other day, and this particular implementation was something I wanted to do for some time.