I have similar issues with our new Epilog FusionEdge. In fact, I still can't get the FusionEdge to autofocus/manual focus for one pass vectoring. The FusionEdge was perfectly sharp when it was first installed, but after a month, it lost the ability to autofocus. No amount of aligning and calibrating the focus/manual focus has gotten us back to the original autofocus capability
Aligning the laser mirrors has helped. These videos were useful in helping me understand alignment and how to do it. While the example is an Epilog, it should be similar to your Universal. Searching for "align laser mirrors" yields many results.
I really like all of Trevor's videos/channel:
Good luck!
- Laurie
Laurie Toyama
Program and Technology Manager,
FabLab Santa Clara High School