In past releases of Revit you may have noticed that moving Reference Planes that had their Origin property checked had no effect on the actual origin of the family. Revit simply ignored this and continued to use the original intersection of these Reference Planes.
In effect the origin location was hardcoded. As a result many of us have made it part of our routine to avoid moving the Reference Planes at all.
Good News!! In my limited testing it appears that the most recent build has addressed this issue.