If you run the "with jitter, perfect knowledge" case, the 3D scene target should reconstruct fairly well. Instead, the 3D point cloud is a mess.
The problem is specific to using the temporally uncorrelated jitter model. The issue has been traced down to some changes that result in one jitter realization being used for imaging the focal plane and a different realization being stored in the BIN file. This is because the uncorrelated jitter model is not deterministic, and some performance improvements to eliminate a deep (and slow) cache resulted in not using the same values for the same query time.
Fixed in the 4.7.0 release cycle.