I just went through them all in turn and Leo started up with the right layout each time.
I tested by putting the setting node into the setting tree in my workbook.leo outline, changing the specified layout, and starting a new session of Leo that opens just the workbook.
I am aware of a problem I've had from time to time where VR (not VR3) doesn't show up. The log pane shows the message that the VR pane has been turned on or off but VR isn't actually visible. As you said, there's a workaround so I thought we could tackle it after getting the layout machinery into devel.
If VR doesn't show itself one might get fooled into thinking that the wrong layout had been loaded - depending on the layout, of course.