Extruder motor making a knocking sound, nozzle is not clogged
A knocking or clicking sound does not imply you have a problem, it implies that you could have a problem; it can be the characteristic of the extruder. 



My own designed 2.85&nbsp;mm filament, 1:4 speed reducing belt driven extruders make clicking sounds while extruding (independent of the layer height), I have verified that no steps are lost and the printer extrudes exactly the requested amount of filament (2.85&nbsp;mm filament requires a lot more pressure for the same nozzle size, the noise is coming from inside of the metal Bulldog housing, not the stepper adjacent, it is not stepper nor filament skipping noise). 



A clicking sound in combination with gears losing position as you describe (or filament skipping back) does mean that the pressure in the nozzle is too big for the extruder to push it through. If the gears loose position, this means that the stepper is not powerful enough to push it through, this means that more current or a more powerful stepper is required (the latter option is due to the design of the extruder not possible). If the filament skips back while the gears are in place the tension/grip to the filament needs to be increased. 

In troubleshooting this problem it is best to increase the current to the stepper close to the upper side of the specifications of the stepper and see if the knocking sounds disappear. This should not be a problem for such a priced and tested extruder system, i.e. considering the reputation and quality of E3D this extruder must work out of the box unless you have received damaged components.