The first thing to check is whether you have a motor bearing that is starting to seize up. With the spur disconnected, does the rotor/pinion in both cars spins just as easily? Next, you can't reliably set gear mesh on the 3s trucks with the power module cover off. You'll have to check with the cover installed. Then your gear mesh should be as close as possible while allowing you to hear slight clicks as you lightly rock the spur back and forth and at various locations around the spur.
If then mesh is set well, and your motor bearing and slipper house bearings are in good shape, then I wouldn't worry. Sometimes worn spur gears make different noises.