DIAGNOSIS That's almost certainly a loose chain or rail. The jerk at the start and stop of travel causes the chain to slap against the rail or the trolley to knock against its stops.
FIX Check the chain tension first. In the middle of the horizontal section, you should be able to push the chain up about 1/4 to 1/2 inch. If it's sagging more than an inch, it's too loose. Tighten it by adjusting the tensioner on the end of the rail opposite the motor unit. Loosen the bolts, pull the rail slightly to take up slack, and retighten. Also, check that all rail mounting brackets to the ceiling are tight.
IF THAT DIDN'T WORK The noise could be coming from a worn drive coupler (the rubber piece between the motor and the gear assembly). If the chain tension is correct and all bolts are tight, that internal coupler might be deteriorated, transferring shock load. Replacing it is part of the gear/sprocket replacement process.
HEADS UP Don't overtighten the chain. Too much tension puts extreme stress on the motor shaft and the plastic drive sprocket, which will lead to a stripped gear and a much bigger repair.