Have you applied any blending mode on any of the layers in the group that you are flattening?
This doesn't fix the bug at all, because this is a directly different behavior than all previous versions. Flattening groups is a common practice among professionals, and no, there are no blending modes in this example. Just a simple soft round brush.
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I wonder if this is an OS issue, or a graphics card issue. I just tried it on my MacPro - running Mac OS10.5.5 with a NVidia GeForce GTX980, and there doesn't appear to be a difference when flattening a group, or flattening individual layers - or when I tried it with Flatten Using Gamma 1.0 off. I do have PS set to use my Graphics processor with OpenCL and all Advanced settings on.
Perhaps more information on your system setup may help us to determine what might be the issue?
Thanks for the video showing your method. I agree, when you flatten to a layer, it does display correctly. However, when I simply flatten a group (without merging it to the solid layer behind it), the falloff changes. I don't think it's my system, since photoshop version 6.0 and cc 2015.5 both display the same before or after group flattening (not merging a group with a solid background).
I just tested it again in the newest cc 2017, and it's still preventing me from upgrading. I'm a matte painter by trade, so painting in groups, then flattening them to take into compositing is the standard workflow.