[HELP] Mission spawned hostile pirate ships resetting to nuetral relations

[TechSY730]

I have this issue where mission spawned pirate ships for "defend base" missions (and maybe others, but this is the one I noticed it for) get set to default relations based on notoriety quickly after they are spawned (aka, neutral to pretty much everyone), breaking the mission. I can confirm they spawn with correct relations (hostile to player and the main races), but don't keep them for long. The odd thing is that this only sometimes happens, some ships keep being enemy to me and the main races.

Is this something that happens in vanilla? If not, how can I find which script or director script is causing the issue?

I've already searched for relation setting commands in my scripts (especially "set relations from notoriety"), and found some issues that needed to be fixed, but the overall problem remains.

I have way too many scripts and mods to list them all, which is part of the problem I know, but I am willing to dig to figure this out.
But here are the big ones that would seem suspicious:
1. TC plots in AP
2. LIFE
3. Improved Races v2
4. A heavily customized version of Military Base Response Revamp (so it no longer conflicts with AP's rapid response fleets, and many other fixes)

I've already combed over these for possible causes, and I think I have fixed those, but the issue still remains.