Do you use Layer Parenting?
If no Layer Parenting or camera are involved, and you like, you can record a video of the issue and submit your FLA for inspection.
What you describe does not sound like a Smart Magnet Rig problem, but rather an issue with Animate.
Of course, if we can reproduce the issue, we will investigate what the causes might be.
Make sure to specify the exact version of Animate, EDAPT Tools and OS.