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I'm fairly new to the Agisoft Photoscan program, but I am trying to build several models using aerial imagery and highly accurate GCPs, with coordinates collected in the field. I align my photos and enter my GCPs, but when I build the model, the GCPs do not seem to stick. When I go to the areas that have GCPs in the model, they show different coordinates and elevations than those I measured and entered. Is there a way to get Photoscan to keep the known coordinates?

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It sounds like your reconstructions are leveraging the GNSS data from both the (not-so-accurate) imagery as well as your ground control points (GCPs).

There is this tutorial here for doing reconstructions with ground control points.

After you have added all your GCPs as markers, and after you have marked all the photos with the marker locations, then uncheck all the cameras (but keep the markers checked) in the reference pane. Next, hit the Update button. This will ensure that the sub-standard coordinates from the drone images are not used in generating the final surface model.
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FYI, there is a user forum for Agisoft here. You will get an informed response from the helpful developers in a timely manner.

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I work the same thing here and I am using the old 1938 aerial photography. You should click on the View Estimated (see red circle)and see if it is compare to the one you have View source.

enter image description here

P.S. Yes I know how you are feeling because I have work on this a lot...

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