By burnover did you mean the resin staining that happens when you do deep engraves? (No way around that, it’s the reason that the proofgrade material is masked. When you remove the masking, that comes off. Gorilla duct tape works really well to remove it on small bits like the dots.) Or did you mean something else?
Only thing I can think of that might cause the lack of roundness might be a slightly loose belt under the laser arm. There are instructions here for how to check and tighten that up.
If that’s not the issue, you’ll want to open a new thread in the Problems and Support section of the forum so support can look into it for you. It should come out round if the file is round.