Hey @MachineRobG , welcome to the forums.
Since your new to cnc machining I’m not sure what you do it don’t know so pardon me if I state the obvious.
My first two guesses are that either your tool height is bonked or you current work coordinate offset is getting changed.
Your tool height could either be wrong in the offsets table or the wrong tool height offset is getting applied somewhere. Notice the green box in the gCode calls out “T3 G43 H3 M6” which applies Tool 3 with Height 3 applied to it. If, somehow you call “T3 G43 H5 M6” then you will apply Tool 3 with the Height of tool 5". You can verify this by making sure the height applied to your tool shown in the bottom right of PP matches the measured height of the tool as well as what is in the tool offsets table. You will want to check these on your cutting tool as well as whatever you are probing your piece with.
If your current work offset is changed when you probe your piece then you could be zeroing the wrong work offset when you probe your part. Verify that the work offset called from your program is the same as the active work offset that PathPilot is looking at (see the red squares). However, notice that the sample program in the screenshot below is using G56 while there is still a G54 listed in the beginning of the program? That is part of the safety block that Fusion is adding to the beginning of the program.
If this is what is hanging you up then you should check out the first few videos listed in Video List - Chapter 1 - Getting Started with PathPilot
Good luck and keep us posted on what you find.