Can't quite see where this is happening, but: If I set up a laser in VAB to point at an origin/calibration boom, say a nice stripey Communotron 16. In the VAB it reports as hitting said Communotron, wheras when in Flight, the same laser will report as hitting the parent of the Communotron.
The distance/ angle of incidence is still correct (and as such, the laser cannot be hitting the parent) it's just then finding the wrong part in the tree, it seems.
It may be related to symmetrically placed parts, but I haven't proven that yet.