I use manual registration and spherical targets. After I have identified 3 or more common targets in adjacent scans, Recap tells it found a match, and then tells "refining registration.." Sometimes the refinement gets confused and arrives at a result significantly off. I suspect that the refinement has an iterative algorithm that does not always converge but occasionally diverges.
Sometimes the problem can be solved by removing a few scans from the registration group and re-registering in a different order, but not always.
I suggest a check box "disable refinement" to temporarily disable automatic refinement and get around the problem.