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Problem fixed:
Just in case somebody goes through the same issue, the solution in my case was to replace wiring of the X-limit switch with a shielded cable.
Regards

I just noticed that the post is not that old, 2015 was the joining date of PropellerHat. Getting old, need better glasses :-D

I know this is a 6 years old thread, but it describes exactly what is happening to my cnc today. Did you ever found the mistery?
Thank you very much,