Alex,
I'm working in EPSG::2054, I have figured out that when "Building orthomosaic" with option "North Up" checked, it does not export Orthomosaic. With "North Up" not checked it exports ortho mosaic, but with Export window and "North Up" option checked, it still gives me south up orientation photos, regardless if the option (North UP) is checked or not.
I have actually restored my PC incase there is a hardware issue, but I'm getting same result as before