It isn't surprising that the new link belt ran more smoothly than the old V-belt. Old V-belts that aren't used get stiff and take a set. Once in a while, after a few hours running, they will smooth back out. However, the best solution is to just replace it with a new good quality V-belt of the proper (same?) size. The trick is to inspect the belt at the joint before you buy it. If the belt gets thicker at the joint or if the two ends aren't aligned, the belt will thump every revolution.