IJ mode is modal. If your g-code has a G91.1 in it, it is changing it in General Config, and it should remain Incremental until you change it, or run code with a G90.1 in it, which will change it back to Absolute IJ.
It's good practice to have your CAM software add the G90.1 or G91.1 to your g-code, which will automatically set Mach3 to the correct IJ mode for that particular code. In almost all cases, this would be G91.1.
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I looked at General Config after loading my code with added G91.1, and the Absolute IJ button is still selected?
I modified my MeshCAM Mach3 Post Processor to include the G91.1. And I emailed a note to the MeshCAM author asking for his input on the issue. I'm guessing a large percentage of his customers are running Mach3 systems.
Paul