I ran into problem with flattening layers. I had a background layer and a curves layer. When I tried to flatten the image or merge visible, the curves layer was not applied to the result. Merge down worked. After restarting PS6 flatten and merge worked
I can't comment on your particular situation without seeing the layer stack, but there have always been times when flaterning produces unexpected results. The workaround is to use a Copy Merged layer at the top of the stack. (Shift Ctrl Alt e or Shift Cmd Opt e)
In some cases (usually adjusting over a detailed, high contrast image) Merge and Flatten can look markedly different when combining the adjustment layer and background. But when viewed at Actual Pixels (100%) you should see no difference.
When you get a chance, try to repeat it at differing percent views.
100% view (that is Actual Pixels) means that every ONE pixel in your image is being represented with ONE monitor pixel. It is the best way to see the actual adjustments ( or sharpening or effects, or whatever) Anything less than that will be subject to view interpolation issues.
The problem is, with multi megapixel images, you can't see the whole image on your monitor at 100%. It will be too big!
Now whydo Flatten and Merge show different previews? That is the question.
The image consisted of kids with a dark background. It was a scanned slide with the dark area showing as a noisy green. I adjusted the curves to make the dark areas black while preserving the image of the kids. If this shows up again as a problem I will try the 100% view as well as save as a jpg which is my goal. Will then look at the jpg in a different program to see if the end result is what I expected.
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