How does the populator work? I noticed (not for the first time, but now it was kind of cumbersome) that if you change the outer perimeter (the extent of the population), the same seed gives you a different instancing.
In this case I didn't need the 10x10k extent, so I lowered it to 7x7k, but lost my 'perfect' distribution. I guess it's not based on some PF base, world spaced?