I am confused by this. I don't use any gradual selection tools in the point cloud process, and the only filter I use is the one in the Build Geometry... dialog, where I leave it at the default.
I have not spent much more time trying things in 0.9.0 because I am re-flying ~60 sq km every ten days or so and that keeps me plenty busy with the image processing, but I finally put together a second computer that I could try to reprocess some data with for comparison purposes if that would be useful.
I have projects that I completed in 0.8.5, complete with GCPs, and I could reprocess the "Build Geometry" step and compare DSMs if that would help with anything. Unless I don't understand the gradual selection process, I don't think that played a role for me.
This problem is still keeping me from switching to 0.9.0.