Hello willfig,
I have just plugged in 3D Connexion SpaceMouse Pro to the free USB port of my computer, then started Metashape Pro and enabled HID-compliant device option in the Navigation Preferences tab.
In Controller selection field SpaceMouse Pro is selected.
After that no unexpected behavior is observed in the Model view of Metashape - the controller works as expected.
Can you please specify, which 3D Connexion device model you are using, which OS you are using and whether you observe different controller behavior in Metashape 1.5.5, if installed on the same computer?