Merging Visible changes color of image!?

using original CS
every so often, like tonight, i've got a file with many layers of hue, bright, color balance, and more. i've gotten it to exactly where i want it, and want to move the whole thing in one piece to another file. so i merge visible. 95% of the time the result is a merged image that is identical to what it was in layers.
but sometimes there are slight but important changes to the color or hue. (flatten image also has the same prob a fraction of the time)
what can possibly be the problem here?

ok, i re-did this operation so it merged the way i wanted it to merge, but still i see differences. but NOT when i view at 100%. i did not know that:
>>What you see when you look at an image at any magnification other than 100% are interpolated pixels and not the actual pixels.>>
this is invaluable info--thank you. still, i dont understand why 95% of the time when i merge visible--at whatever magnification--the image looks the same.

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