Hello Filip, hello Dieter,
Please confirm, if the problem is reproducible in Metashape Pro 1.8.4.
Filip, please provide the screenshot of the Reference pane section with the markers, so that the checkboxes and source coordinate values are visible.
I am not getting such problem in 1.8.4 for markers without projections (but with source coordinates) used for Planar/Cylindrical projection definition.