As you know, there are several differences between objects created with RailClone 2 and RailClone 3 (you can see the details here
Under normal conditions, RailClone detects if the object were saved with RC2, and upgrades it automatically to RC3.
But several users reported that their scenes were not always upgraded.
After some investigation, we noticed the upgrading process fails when the scene uses any XRef Scene, regardless of the scene's content (even if XRef Scene is empty).
According to our tests, this seems a 3DS Max bug, and we have reported it to Autodesk.
Unfortunately there is not a workaround, except removing XRef Scenes before loading a RC2 scene.
Please note that once saved with RC3, objects are considered as "upgraded", even if the upgrading process didn't work.
For any question about this issue, please ask us in the RailClone Pro forum. Thanks.