If you enter a Z-axis offset, it's going to physically shift all of the coordinates in your gcode file by that amount (starting and ending scripts excluded, since you can customize those coordinates yourself). So slice your file and click "save toolpaths to disk", then open the .gcode file in a text editor. Scroll down to layer 5 or something and look at what the Z-coordinate is. Then go back, enter 10mm for the Z-axis offset and repeat this process. You should see that the Z-coordinate is 10mm larger at layer 5.
This will prove that the software is creating the correct gcode files. If it is, and the printer is still printing layer 5 at the same height, then it would mean that something with the firmware is getting in the way.
PS - I'm specifically using layer 5 so that you don't accidentally get confused by looking at first layer stuff. So make sure to do this test with a higher layer (i.e. not layer 1, 2, or 3

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