For the specific save I've tried the most to work around; I've got a character with a Tri-Tachyon commission. I want to backstab Tri-Tachyon and steal all their planets since I've gotten all of their ships and weapons to the Omnifactory. I have one big problem. When I invade one of their planets I get an infinite loop of "Your commission with Tri-Tachyon is annulled!" Eight to ten notices posting every second for as long as I cared to try and play on. In about 15 minutes of time accelerated play the repeated notices showed no sign of stopping. This happens regardless of if I invade them with or without leaving the faction first. All other faction relationships seem to default appropriately, however.
I've started multiple games with different faction commissions, the problem appears universal across all factions. I tried waiting for a long period before invading, but the same issue reoccurs. I can provide my save file on request. I did not open an issue on the bug tracker because it wouldn't let me for some reason.
Representative screenshot:
http://www.ultraimg.com/image/wNi0Enabled mod list (If one of these is a known troublemaker, I'll eliminate it and check again):
Starsector+ 3.3.0
Blackrock Driveyards 0.8.2
Combat Chatter 1.4
Common Radar 2.2
Console Commands 2.7
Diable Avionics 1.61
Interstellar Imperium 1.10.2
LazyLib 2.1
Nexerelin 0.7.4b
The Knights Templar 0.9.5f
ZZ MusicLib 3.1.0+
ZZ ShaderLib Beta 1.2.1