Is the change apparent when merging at View > 100%?
cp is right. Anything with heavy noise must be viewed at 100%. The on-screen preview is calculated on the basis of the screen image. At other zoom ratios the image is softened by scaling, and the calculations affected by intermediate values that aren't there in the original.
That said I think you're approaching this in an unefficient way. Try reducing the noise in ACR/Lightroom with the raw file first.
I've not tried shooting at 12800, but I have a few 6400 shots. This is out-of-the-camera first, then noise reduction and sharpening in Lightroom (ok, maybe I overdid it a bit, but just for demonstration...). Click to see at 100%:
You're absolutely right! At 100%, the merged layer looks identical to the layer stack. I'm amazed as to why that is.
The portrait photos shoot at 6400 look very good. (Actually, I should have been able to shoot at 3200 or 6400 instead of 12800 had I been paying more attention to the camera and less to the fish.) Thing is, for this shot, I would like to be able to really emphasize detail, and I have never been able to do substantial noise reduction with no loss of detail. I wonder why ACR does not allow us to mask noise reduction like it permits us to mask sharpening.
Many thanks for the help. Much appreciated.