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GCP site calibration transformation not applying and graphical bug

I have a project that is using an arbitrary GCP & output coordinate system with geolocated input images. I have applied GCPs that have been transformed to my own coordinate system and enabled the Site Calibration of where the optimized parameters have been loaded.

However the GCPs are still far in the distance even after re-optimizing and completing the processing all the way to mesh. This is causing major display issues with everything also due to the distance the objects are separated by. My dense point cloud looks like a sparse one and at different viewing angles only half of objects become visible.

Can someone please explain why the transformation isn’t being applied and how to solve the heinous graphics issue?

This is an industrial survey trial using the Pix4Dmapper Pro trial, processed on a an HP Z800 with a Quadro 4000.

Looks like your transformation may be in error. It would be simpler to use the old option to pick your GCPs instead of the ray cloud. Also, are you sure your units are the same.