I have tried but can't reproduce it with an unmodified version of the mesh so far. It only happens 1/30 or so with a modified mesh, and even with different kinds of software.
I export the model for cleanup, steps of retopology etc. When I import it, most of the time it aligns correctly. But sometimes it comes out of alignment, how much, seems completely random. Rotation and location can be slightly, or completely off, but scaling is always the same.
Sometimes, when I reload the project file and try importing again, it aligns correctly, sometimes it doesn't. Then all I can do is to export the mesh I currently have in the project and continue working (which is a reason I save often) Sometimes, I can reimport an older version of the exported mesh, but at other times, they are -all- out of alignment, except for the one already in the project file.