When I install this mod my game automatically crashes when I want to start a new game, but when I deactivate or uninstall it, I can play a new game without any problem

I think you have your virtue / affliction chances set incorrectly.
(iris2B.info.darkest => line 168 & 169)

You set:
iris2B_system_breakdown .override_trait_type_chances 3
iris2B_ego_manifest .override_trait_type_chances 1

That means System Breakdown has a 300% chance and Ego Manifest has a 100% chance.

.override_trait_type_chances needs to be a percentage (ex. 0.5 = 50%)

They are base chance. Not percentage chance.

Hmm... That's odd, because the flagellant has his .override_trait_type_chances set to 1.0, and that causes him to always enter his custom affliction.

Maybe I'm wrong, but I've never seen my 2B virtue so I thought that might have been the cause.

So your saying it takes 3 / (3+1) = 75% for system_breakdown and 1 / (3+1) = 25% for ego_manifest?

Yes, it should work the way you mentioned (and I'm pretty sure it works that way because I tested with affliction/virtue back in the day).