I own a PlasmaCam machine...equipped with the Hypertherm Powermax45 (equivalent power to the Lincoln plasma). Cut quality is excellent, square, clean edges up through 1/2", excellent consumable life.
The Lincoln is a relatively low duty cycle plasma designed for hand cutting. Many are used for mechanized cutting......but reports of poor consumable life, bad cut angularity and exceeeding duty cycle (power supply shuts off) are fairly common.
Best bet is to contact Lincoln directly.....maybe they can work with you on settings for cutting each material thickness.....such as speed, pierce height, cut height, pierce delay time, etc. These will help with your issues.
Here are pics of some cuts from my PlasmaCam with the Hypertherm plasma...