Hello toffersan,
Can you please specify the following:
- are you using the chunk alignment operation or you are merging the chunks basing on their georeferencing information?
- are the coordinates applied correctly in each chunk using Update button on the Reference pane before merging?
- which chunks you are merging from your first screenshot?
- also provide the screenshots or text files with the coordinate information (source values) for each chunk before merging.
For mee it looks like there are some invalid coordinates in one of the chunks for the disabled cameras (like 0,0,0) so on the first screen valid cameras are placed to one point and invalid (light-blue sphere) - to another. The distance between such points in geographic system is very large, but by default PhotoScan is trying to display all the camera positions, so it looks like all the aligned cameras are stacked to one point.