Did you test the following scenario :
Move the bed down so that it is at least a couple of inches or cm away from the nozzle
Heat up the hot end to 200°C (or above the minimum extrusion temperature)
Feed some PLA
Move to > 150Y and extrude using i.e. move axis/extruder commands on the LCD : extrudes ?
Move to < 150Y and do the same : extrudes?
If it is 2 times yes then it could be a bed leveling issue. When touching the bed or the print with the nozzle, the plastic can't extrude and the extruder will have problems pushing more filament into the hotend. The clicking will be step skipping due to that.