For anyone experiencing this problem, here is the solution we found to the problem. Data were being added as feature services to Map3D using the ArcGIS Connector from an on-prem ArcGIS Portal. The issue described was found to only occur on layers that had z-values enabled. Data in geodatabase/feature service were UTM83-10, feature service was UTM83-10. Drawing was set to UTM83-10. The problem was that the ArcGIS connector defaults to LL84, no matter what CRS/projection is set in the drawing or feature service. The solution is to run the MAPARCGISCONNECTOROPTION command, and select '2', the option to use the coordinate system that the drawing is set to. I'm not sure why the ArcGIS Connector would default to a projection that is different than both the drawing AND the published feature service, but it is.
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