What is the starting system of your force-spawned empires? It has to be Random if you want them all to spawn. The game will not reuse starting system, so if you use any other starting system for multiple premade empires only one can spawn. This includes using other starting system that have "random" as part of their name like Random Trinary II and Random Binary I. Those aren't truly random and count as specific systems. Only Random really counts as random by the game and can be reused.
I quickly tested my own custom empires and I could easily force-spawn them all with no random empires added, but I do make sure they all use Random starting system.
Already checked it, that's not the problem no matter how many people keep trying to point this out, it's NOT the issue. It doesn't seem to always appear, I am not sure what the difference is though, I suspect one of the origins causes the problem, but based on the 20+ tests I did by now, I don't know which origin causes the issue.
I did it with all hive minds, no hive minds, two relic world starts, no relic worlds starts, it appeared regardless. The one case where it didn't appear was when nobody had a special starting planet and there were no necrophages either.
UPDATE with screenshots, I am baffled by what it could be. This is extremely extremely weird. I tried SO many tests and it's still inconclusive what causes the issue.
The origins were my primary suspect, that maybe Remnants and Life Seeded conflict with each other, but nope, when I used two devouring swarms they couldn't spawn together.





But when I replaced the devouring swarm relic world start with another empire that doesn't have devouring swarm they did spawn correctly:

So then I tried what if I used the same empire, just replace the government trait from devouring swarm on that same empire, but they still couldn't so it can't be the devouring swarm trait. I tried changing them from a hive entirely and they still couldn't spawn together. Something else is causing the issue.

They don't share a portrait, one is avian the other is plantoid, they don't share names, they don't share origins, they don't share home systems, they don't share colours or ship sets, they don't share anything. So I figured, screw it, let's change the portraits, I changed it to a fungoid and then the portrait is bugged out, it shows the old one on the side, but the new one in the middle, but also they do not spawn together still. But the slight visual glitch did fix itself later.
The bug seems to start when the empires are first created, as when I 'rename' the Husk Horde over here to Husk Horde1 it of course creates a new empire on the list and that one CAN spawn with the Carrion Swarm.
So even if I edit things on the Husk Horde, it doesn't matter anymore, those two refuse to spawn together no matter what. The only way to get the empires to spawn together is to make a new one.
So here's what I did, I changed back everything on the Husk Horde except renamed it to Husk Hordes with an s and then they both spawned as normal. So please stop telling me it's the homeworld that's bugged, it's not, it's this entire empire for absolutely no reason, and who knows how many of the other custom empires I made also share the same problem that literally can't be fixed unless you make a new empire.

