Race Starting Percent Migration: = 1
Race Migration Added 1 Percent Per Population Amount: = 3000
and it has the effect you wanted.
Check the population on your colonies: how much is the migration in %?
Did you make any treaties that allow migration between empires? That can lead to a substantial increase of the population.
Has migration been fixed to allow complete migration and undoming of a planet? I remember previously planets would stay domed until player intervention got rid of the non-breathers.