3MX not working properly with other georeferenced files

Hello,

I'm trying to attach a 3MX of a work site and then import some georeferenced shapefiles and a DGN containing some 3D solids into the same project. They should all be in MGA 1999, Zone 56 (Australian projection).

When I attach the 3MX by itself the model sits where it should in georeferenced space. I've checked the extents and a bunch of features within the site and they are correct.

When I import the shapefiles and the DGN containing the 3D solids, they also site in the correct space. I've checked the coordinates of the objects and they are correct.

When I attach the 3MX and import the shapefiles and 3D solids together, the shapefiles and the DGN shift by a huge amount and nothing lines up. When I go back and check the coordinates of the shapefiles and 3D objects they appear to have shifted by 10's or 100's of thousands of metres.

If I import the shapefiles and 3D objects with an attached 3SM, generated from the exact same project, everything lines up. Does anyone know what could be going wrong here?