Hi Alexey,
The imagery is flown with a wide angle camera (11.5cm lens on a 18 x 18cm format) at 25,000 feet so the raw GSD is about 0.94m. The control is accurate to +/-2m in XY but to about 0.2m in Z.
What is happening is that I am getting a reasonably good set up (Alignment / AT) and even right through the process, getting errors in the +/-4 - 5m range which I am expecting. When I check the orthos in Agisoft after the build, with the control positions overlaid, they are all quite reasonable and expected given the GSD and the control accuracy. When I export the orthos from Agisoft however, the orthos shift their position which I have never seen before. That is my problem!!
The attached files show two different points at opposite ends of the project. The "Agisoft" files show where the control point falls when the control is viewed within Metashape itself. The "Global_Mapper" files are where the exact same control file is viewed over the exported orthos when loaded into Global Mapper. The images have shifted. Why?