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I just flashed my new Ender 5 with Marlin and I had the same issue. The 2nd and 3rd layers were digging into the previous layers.
I manually lowered the bed by 10 mm via the machine knob and the bed only moved 5.207 mm (I used a dial caliper). I went into the EEPROM and adjusted the steps/mm for the Z from 400 to 769:
10 mm /5.207 mm is 1.921
400x1.921 is ...
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