If your talking about the "J" in the G2 or G3 commands, there is also an "I" value that accompanies the "J". They specify the center of the arc. There are two modes that are available for specifying I&J in your Mach configuration. Absolute and Incremental. You should be aware of the methods your cam program outputs, and make sure that both it and Mach are set the same. I&J can also specify the endpoints of arcs, distance from start-end of arc, and other confusing methods of arcs. However, I *think* that Mach only interprets them as arc center points, using two methods.
I loaded your code and did not see any obvious errors that would make a deep plunge. Did the plunge happen at the same points both times, or at a random place?