Shapeoko 3 Xl cutting depth problems

Looking for some help with my Shapeoko 3 XL
After I create my toolpaths and save the toolpath file and save my complete file and run a test and find I cutting a little to deep. I go back to toolpath and change the cutting depth, save toolpath and save file. Load into motion and when I run the file, I get the same depth as before. I cutting at a depth of 1/64 to 1/32 This is a problem I been having for some time.
I had done one project earlier and everything went fine. Just don’t understand what I’m doing wrong.
I have gone through setting up the correct options for the machine.
Any help would be appreciated.

Which Z-axis does your machine have?

What toolpaths are you cutting in what material using what tooling?

Could the tool be pulling out?

Which controller does your machine have?

How are you measuring?