Either I have not understood something here or this is a bug...
1) Display a 3D view.
2) Display '3D View Settings Dialog box (Settings->3D Settings)
3) Under 'Settings' tab, check 'Exploded View of Layer Stack'
4) Undo the above change - uncheck 'Exploded View of Layer Stack'.
5) Under 'Layers' tab, make some changes to the check/uncheck settings for some of the layers and 'Apply'.
What happens is that the checked or unchecked tick boxes applied in step 5 change in an apparently random way when 'Apply' is clicked.
Clicking Apply after steps 3 or 4 (or both) makes no difference.
I suspect there could be an uninitialised variable somewhere in the code.