Yes, once you pick a new spot to use Set Focus on, everything else is going to shift a little.
Just want to make sure you understand what is happening…when you use Set Focus in one spot, it temporarily transforms that area into a “directly under the lid camera” view. So you can place whatever design you have in that spot accurately.
In order to place the stuff on the other side, you use Set Focus there, and it will give you an “under the lid camera view” in that spot. You place that design, but then all of the other ones are going to look like they shifted. They did not actually shift, just the image on the computer screen changed. (It is generated by an algorithm - the actual shot captured by the lid camera is HUGE and very warped. The Glowforge interface corrects that view for us and sends the image back to our computers.) Where the actual engraving is going to happen on the material on the bed (which is what is important) does not change. (Even if the view of it does on the screen.)
This is what they see:
They will convert that using the algorithm into what you see on the interface. The trick is to use Set Focus if you need accurate placement out at the edges of the bed, place your design, and then ignore it when the rest of the view shifts.
(Might be more than you needed to know, but I’m not sure how far of a shift you’re talking about.)
The view also always resets after a job is run. That might be what you are seeing.