Looking at the help topic Insert a Point Cloud File I'm seeing the following description for the Auto – By Shared Coordinates Positioning option when inserting a Point Cloud:
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Auto - By Shared Coordinates: Revit assumes that the coordinates in the point cloud file are specified in the shared coordinate system used in your model. As a result, the point cloud origin will be placed at the origin of the shared coordinates that can be accessed through the Survey Base Point. The point cloud will be oriented so that the north direction in the cloud file (0,1,0) will be mapped to the True North of the Revit model.
Note: By default, project origin and shared (survey) origin are in the same location. When you link a point cloud file, the end result of selecting Auto - Origin to Origin and Auto - By Shared Coordinates will be identical.
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Based on this information, I would suggest first checking if the Survey Point in your project has been moved away from the Project Base Point.
Additionally, is the location of the Survey Point where you want the origin of the point cloud to be placed?
Lance Coffey
Technical Support Specialist