(Scene 6.2) is mostly very helpful software, although there are some very serious bugs involved within it when using it in a high-accuracy survey format.
The biggest I have found is when applying survey control to the point cloud. Scene calls it referencing. For some reason, at totally random occasions, it moves the raw survey control to a totally different control network. The greatest error of move I have had is 150 meters in the northing and easting, then 42 meters in the height. And as it has moved the raw survey control it still tells you this is mm accurate. For a survey company this is catastrophic. I have written to faro with no reply, as of yet.
The only way I have found to correct this is to go to the properties of the main scan manager folder, go to the transformation section ad set all global co-ordinates to 0 zero including the height. Then re-do your target recognition and subsequently re-apply the referencing target registration.
Hopefully this fixes the issue and I hope this has been helpful to anyone with the same problems.