Many driveshaft shops are notoriously sloppy when it comes to welding the yokes on the tube, that's why they have to balance them. I make my own shafts in a lathe and install the yoke so there is no runout at four points perpendicular and horizontal to the u joint cross. I've never had to have a driveshaft balanced when doing it like this.
It sounds like your shaft just has too much runout.
