Coolhand,
If there is something mechanical, perhaps it would be easier to define by cutting a larger part? Maybe a 12" x 12"? I would be curious to see if the results were still consistent with the 4" x 4" part?
Here is some info that might help. The section on bevel is on page 9 of the PDF file.
http://www.centricut.com/Articles/Ce...g_Articles.pdf
Setting the parameters for the best plasma cuts can be a challenge. As you mentioned changing one affects the others. Since the plasma flame is flexible and spinning in a circular motion it takes some getting used to when you have been accustomed to cutting with a rigid tool such as an end mill.
Understanding the characteristics of the plasma arc in relation to cutting heights, speeds, short paths, circles, different thicknesses etc. along with hands on experience will be the fastest route to the best cuts.
Also take a look at parts cut by other shops to compare to yours. You might be surprised at what you see.
Magma-joe