I posted the new mapfile zip, same place as the Last one.
http://benatar.snurgle.org:8080/~fluffy/pantheons.zip
I unset the "scenario" flag, so now normal game settings work. I really do not think there is anything wrong with Machaka or Tien Chi starting positions, they seem to be working fine to me.
I also kicked out the Mictlan pretender, so Tauren can re-upload a correct one.