Alright, here are my findings:
Firstly, I think the choice of map may have been bad. When I started the game, I chose Egypt, and started in Egypt. But I also noticed that there were limited civilizations (America, Arabia, Aztecs, etc. were not available, which means I was limited to the choices available, which probably means that these civs will start in their own territory anyway) so that was the first problem. I should also note that, in WB, all of the civs started in their ethnic homelands.
Second, again, there was lag. And I know you mentioned that lag meant something was happening, but honestly this was EXTREME lag. I am currently developing a mod with fully-flavored civs, and a lot of python and there is basically no lag when I run it. This had TERRIBLE lag and was at the gamestart, so to me that is not good.
So to sum it up, I chose Egypt, started in Egypt. Had only civs that are available in Rhye's early game, So in my estimation, the map is at fault, because as far as I know the starting locations are pre-set for that map. I think what you need to do is go back to an Earth map with NO pre-set starting locations and work from there. And just to make sure it isn't only my computer why don't we use a small map with only like seven to ten civ slots?
P.S. The reason it took me so long is because I wound up going out drinking, so I just got home.
EDIT: Maybe try to set all of the start points in a known location, like maybe Australia or Greenland or something just so we know it's working.