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I have used that workflow many times before and it never gave me this same problem, or at least never to this extent.

I have tried your suggestion to no avail.

[ATTACH]66836[/ATTACH]

On the left is the picture without that group you suggested. On the right is the exact same thing but merged all.

One things that I have noticed though is that when I zoom into the picture there is no difference between the two. I've lost a little hope with this and am resigned to thing that the photo I took was not of good quality in the first place.

Still is mind-boggling, how the merge visible doesn't give you exactly what is visible though!