It can be difficult to diagnose problems with a laser machine... Since the problems are occurring due to time in usage. It is a fact that the sealed glass laser tube will change performance efficiency as the laser tubes changes temperature.
1) what is your cooling system?
2) what is the water temperature at 5 minutes of usage?
3) what is the water temperature at 15 minutes of usage?
4) what is the temperature of the Laser Power Supply during these projects?
5) is the laser machine powered by 110VAC or 220VAC?
What is the condition of the lens and mirrors? I have experienced that glass dust and some oxidative on the mirrors can heat up and change the reflective properties of the mirror surface.
Can you please clarify the term "jagged edges". I think that most of us are assuming you mean the edge of the material that resembles the edge of a USA quarter. This is commonly called the "coin effect".
I have also seen the stepper motor heat up and the drive transistors not correctly do the micro-stepping. The result is that we don't get a diagonal line... We would see what looks like stair steps.
I hope that that my experience is of help to readers.
Thank You,