I also vote on something loose in the machine.
I looked at the ProBotix Nebula machine and they don't say much about the guides. OK I just noticed they are round guide rails. Check alignment and adjustment of the trucks on the rails.
Check the adjustability of the guides - they might be too loose. Check all 3 axis's
Check the connections between the stepper motors and the lead-screws - make sure they are tight.
In the linuxCNC - look into the acel and decel particularly on the "Z" axis.
There is something going on in the machine.
That is not a programming issue. Nothing to do with stepover or anything like that. It also not an issue with your model, It's almost certainly a machine issue.
That machine should be able to handle that job with ease.
Was that a kit built?
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