Warning: long explanation incoming.
There’s a camera on the lid of the machine pointing at the crumb tray. It takes a picture of your material, which shows up on the GF application, bordered by some rulers, and you line up artwork with your material that way.
But how does the Glowforge know how big or small to make the camera picture so the rulers are accurate and you’re lining up your artwork with a life-sized image? After all, the same 4 inch square of wood would look larger than 4 inches if it’s closer to the camera, and smaller than 4 inches if it’s further away from the camera. That’s just how vision works, right?
It can only scale it to show up as 4 inches on your screen if it knows EXACTLY how far away that wood is from the camera. Since the distance from the camera to the crumb tray is a known number, the only unknown is how thick your material is.
If you use Proofgrade materials, the thickness is programmed in. It’s still an approximation, since every piece of wood or plastic varies a little from the next, but it should be pretty close. That means the camera picture will be scaled pretty close to “true to real size”.
But if you put anything else in the machine, it won’t know, and the picture won’t be the right size. If you line up your artwork with that picture, it will print somewhere other than where it shows on your screen… unless you provide the material’s thickness.
You provide that thickness by measuring it, or asking the Glowforge to measure it. The “Set Focus” button under the 3 dots icon in the menu tells the Glowforge to go measure the material height using its laser range finder on the bottom of the print head.
If you don’t use the “Set Focus” button before hitting the “Print” button, the first thing it does is go and measure the material height on its own, picking a point near the middle of your design as the place to measure it from. That’s what it means when it says “autofocusing on your material”, the first part of the “preparing” stage before the time for your print pops up.
If the measurement it comes up with is different from the height of the material you had selected, you’ll see everything “shift” on your screen as the camera image is scaled to true size. But if you had already used the “set focus” button before lining up your design with the picture, the image is already scaled, this step of “preparing your print” is skipped, and there will be no shift.
TL;DR: Use the “set focus” button before placing your design!