I’m so sorry you’re running into trouble, @gmikewilliams. Could you please take a look at our troubleshooting guides for Alignment and Cut didn’t go through material, and let me know if these steps help?
Regarding the greyed out area you see in the app, there are a few reasons this area could change. First, you will see a different printable area based on whether you are cutting or engraving. Second, the printable area will be reduced somewhat when the head is moving at higher speed, as it can take space for the laser to decelerate. Last of all, the view of the bed will change when the material height is changed or if you manually select a type of Proofgrade material other than what was detected. It might be helpful to decide on the final placement of your design after making all the necessary changes to settings for your print. Please let me know if that works better for you.