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GCP elevations not reflected in pointcloud

Does anyone know why the elevation of GCP’s isn’t the same elevation when they are exported to a point cloud? Seems like the elevation of those points should be consistent between Pix4d Desktop and the exported point cloud in Autocad, but they aren’t.

If I correctly understood, you have included Ground Control Points (GCPs) in a project in Pix4D software by marking them in images and reoptimizing (Process > Reoptimize) the project after step 1. Initial Processing. Then, you have created a densified point cloud during step 2. Point Cloud and Mesh. You have imported this densified point cloud in AutoCAD with the GCPs and they do not align in AutoCAD. Is this the issue you have described? If not please add more information and if possible screenshots. 

The problem might be with how the coordinate systems were defined. I would double check the coordinate systems both in Pix4D and AutoCAD. In Pix4D I would check if the GCP and output coordinate system are defined as they should. Here is an article on how you can check them: 

Maybe the vertical coordinate system needs to be modified, which could explain the shift you are seeing. 

Let us know if you could solve the issue!