When the "Z home" command is issued, the axis will rise, then fall again to nozzle height (as you would know already) or, if the Z axis is away from the bed, it will fall, then rise then fall again to nozzle height. What might be happening on you machine is, when the axis lifts away from the endstop, the microswitch may not be breaking - it has to break before it can drive down again. I would put a meter on the switch, click home, and see if the switch changes state when it lifts. If that's the problem then moving the switch around may help.
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