I too have been perplexed by layering of late, all GREAT suggestions given here to help but you can maybe also try this:
If you are using Hex Parametric meshing algorithm, could you report to me what weighted % inflated you have currently have of the poorly layered mesh (procedure found here).
And then change one parameter, ‘Max face aspect ratio for layers’ to a value of 100 or higher, then make a mesh and then report back here on the new weighted % inflated of the resultant mesh.
I am trying to figure out if the discussion here about CFX solver aspect ratio limits would help here and if this is the correct parameter that we can test changing aspect ratio on.
Also, you may find some of my personal meshing strategy found here, helpful. It looks to me that item 12 would be helpful for your layering.
Dale