I remember this problem with mine, it would track side to side for a bit but eventually would settle, it has to do with the mounts tracking like you said but was more based on balance and flexure. Is your balance good??? or is it too much weight for your eq5???
If your motors are out and the siderial rate isn't tracking correctly aka too slow too fast, take your mount back and get a new one as your mount is fubar.! the reason why i say this is there is no adjustment for speed in a Synscan controller that i have heard of yet, sure you have some adjustment with eqmod/planetary softwares but don't rely on that to get you though the night!
As for your Mechanical side of the mount, if its all quiet then your gears are meshing correctly. As for backlash grab a hold of the mount does it feel like its slapping... how do i explain that one

grab the RA and the DEC rotational shafts and try twist them by hand, if it moves then stops suddenly thats back lash how to fix it, theres a load of stuff on the web about it (quite easy to adjust). but still... take your mount back and get a new one save yourself the troubles