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Am I Understanding This Correctly?

Making a few programs for a part family that just has differences in overall part height. When I check the geometry of the model before programming it matches print. however, when I start making measurements then go to dimension, my nominal number is skewed.

For instance, when I check the model, the dimension is right on to what the print states. Print says 5.500", model says 5.500". But after alignment and measuring, when I go to dimension that item, Nominal has changed on the model. Now, instead of showing 5.500", nominal while dimensioning is 5.480".

Why is that? I don't think I'm doing anything wrong. My basic dimensions all match on positional stuff. Is it just because the part is measured? But shouldn't the CAD geometry still be the same while dimensioning? Kind of banging my head. Hope this makes sense. Thanks for your time.