Ok well if your sure it's returning to WC-Zero (forget MC-Z) after the job as finished and no steps are being lost then it must be the table or machine frame. (provided tool is secure in spindle)

The bed may look flat but if it's not exactly parallel to the cutter across the whole area then you'll get this issue. That's why you should surface the bed to be sure.
If you still have issues after surfacing then I'd be looking at the machine frame and if it's twisted etc.!