Why is Flux Stone not generating?
Solution 1:
I have noticed this in the latest release too. I think the problem is that setting the Mineral Frequency to Everywhere makes the world generator go a little overboard with the minerals. It ends up replacing most of the flux stone with minerals. If you just go with a lower Mineral Frequency (I suggest Sparse or Frequent) you should get more Flux Stone.
Additionally there is a minor bug across numerous versions which causes the finder to not be able to find flux on "mineral everywhere" maps even when there is plenty. This has been tested, and after enough embarks you may get a feeling for the types of area which would have this material without requiring the finder.