Have you tried Merge Layers instead of Flatten Image?
I just tried that and it still is changing the image. I rebooted my PC and even tried the same photo file in PS on my Mac - same thing.
I will try re-building the image from scratch to see if I can get rid of the problem.
Layers can indeed change according to the order in which they are merged.
In other words, try merging them in the order that you created them.
If you zoom in (100% or more), does it still seem to be displaced?
I've noticed a similar occurrence when I stamp visible on a large layered document, usually when doing a final high pass or something. If I click the new layer on and off it seems to shift barely, less than a pixel. However, it seems it's actually an optical illusion; if I view it at 100% it doesn't happen. I tried to figure out what it was, and eventually gave up since I came to the conclusion it doesn't actually affect my final image.
You nailed it! When I zoomed in to 100% and flattened it there was no change. I then printed it both full and flattened and they were the same.
The image was a 3 pano stitch from an 80mb back and was a very, very large file and it was creating an optical illusion.
Thanks for the heads up.
Sorry. I tend to forget periodically that some users try to judge images when they're viewing them at any other percentage than 100%.
All other views are not valid. At less than 100% you are discarding pixels and rearranging the image. At more than 100% you are inventing pixels (making them up).
Never a good idea.