I am having a similar issue. Coordinate system is set correctly for output, everything looks great in RC, minimal positional errors for ground control points but the orthophoto is not in the right spot when exported.
Project is about 1000 photos, about 20 ground control points- most with very high accuracy position and level- either static GPS or total station traverse for X,Y and digital level for Z (so maybe 5mm error at worst) Couple of GCPs only RTK GPS (so ~20-30mm error)
When I bring output into GlobalMapper it looks great (and coordinate system is correct) but then when I overlay ground control points from survey file, their position is not quite correct- not major errors, but in some cases up to 800mm off for position, Doesn’t seem good enough when I consider the minimal errors reported for control in RC.
I have rectified the output in Global Mapper and it’s now spot on, but I don’t think I should have to be tweaking the output from RC to get it correct?!?