I've removed all mods and am now readding them one by one, playtesting after each. Vaynar is not the offender, neither is one city to rule or the Carian Republic. Readding Fervor next. When that works as well, the factions are all clean.
Only a few pieces, mainly the changed UI parts, the new treaties and two fixes, not the rest of it.
Thanks, one of these days I'll need to put up a list of mods I'm using (a lot) and ask the experts which of those should better not be there, because of being buggy or outdated.
Is there a way to make this work with the Vaynar mod ? Vaynar faction cities are still stuck at level 5, while the base game factions work perfectly.