David,
I suggest to run the 2 population version with an upper limit for Theta of 400 and also cut back for the migration parameter to somethin like 400 or 40 because a Theta=400 and M=40 will lead to 4Nm = 1600 which seems _very_ high.
for the manypopulation run I would use an even lower upper bound than for the two populations model, but if you do a model selection with migrate
then you could actually compare which model 2-pop model vs 6-pop model.
Your bounds are too high and this leads to histograms that peak at or near zero because the histograms has only so many bars (default is 1500).
In addition: you use a rather old version of migrate the currently supported main version is migrate 5.0.3 (but I still lack a windows binary, for that)
Peter