Hello Johan,
It is better to use GCPs in their original coordinate system.
So before importing GCP data it is necessary either to convert camera coordinates into new coordinate system using "Convert" button on the Ground Control pane, or to remove/uncheck all cameras in the Ground Control pane. After the previous step is done the coordinate system should be properly set to the one from GCPs using Ground Control pane settings. And after that the marker coordinates should be imported or input manually.