We place markers from photos, double click on the photo, right click on the area where we have little dots painted on the skin, and Place Marker from the menu. So we place Marker 1 on all 20 chunks, then marker 2 and 3, then we align chunks using those makers. Although in some cases we need to compensate as some of them should be moved due to skin movement.
For now we reverted back to version 1.2.5 as it works there perfectly, waiting for the fix though, as we are very limited at the moment
Here you can watch the same markers but placed in version 1.2.5 on the same model. See how they are all on the surface of the scan, where as in the most recent version they just fly around the area, some inside the mesh and some hovering over the model
https://www.dropbox.com/s/cvqbscocwu85eb2/markers_1-2-5.mp4?dl=0