I started an insane galaxy with me + 50 random factions set in teams of two, but no teams were assigned. Thinking I might not gave put myself in a team, I restarted with teans if three, ut still no teams.
finally I opened up prefs.ini &manually assigned teams of three. Upon starting a new game after that, teams were properly assigned to the random factions.
on a tangential note, it would be nice if we could just set "randonly assign x many teams" and have it assign the selected factions into x many teams of roughly equal size as numfactions/numteams fits.