AI units tend to pause at waypoints. There's not much you can do about it.
If the convoy is moving along a road just put wayoints at the start and finish, they'll work out the rest for themselves. If it's a long way put just one in the middle some so that they don't get lost, but basically you want as few waypoints as possible.
If the pausing thing is really driving you nuts you can forget waypoints and use markers and move commands instead.