The FallBack code is clearly causing issues. If you see my above post, when I reverted the functions to return nill instead of pFallBack civs began spawning in a similar fashion to how they have in previous release versions. This is after I reordered and change the fallback score priorities and had spawning too close to another minor and major civ as the first checks after impassable and water.I didn't get much chance to look at this last night, as I actually had a stint playing the game. But the more I look at it the worse it gets. I haven't even started on the fertility function yet!
If the minimum distance has increased then it tallies with what I have been seeing. After getting a few "too close" starts I tried moving the minimum Civ distance up the priority chain of the fall back code. Which only increased "too close" starts and made them closer and more clustered so I assumed it was failing more often and reverted. I should have checked the minimum distance parameter d'oh.
I will hopefully get a good run at this tonight. If it goes well and I continue tweaking then I will have to decide at what point this is just fixes and at what point it becomes a separate mod with improvements.
Feel free to keep messing with this, as I would like to see you made the fallback code work. Once you start looking at fertility, let me know if you can find where bonus resource fertility values are stored. I would really like to tweak those values but I have no idea where those values come from.