Couple of things to check. If you turned between a 60 degree live center and a 60 degree dead drive center and still ended up off center; Did you have any dry glue inside the tube? Did you chamfer the inside of the brass tubes after you squared them up, and how consistantly? How did you square the wood blank to the tube? How tight did you have the tube between the centers?
Oh, just thought of this one, were you trying to turn both tubes at once using a three piece bushing set? I've never heard of anybody making that work, we almost all turn one barrel at a time between two bushings, (if we use bushings at all)
Dry glue inside the tube will cause the tube to not seat evenly on the bushings (or centers) , as will the ragged inner lip of brass left by a pen mill, or an uneven chamfer. An inaccurate or incomplete job of squaring the blank to the tube will cause bushings to seat inaccurately as well. In theory if turning between centers with no bushings this would not be a problem, as the centers only contact the inside of the tube, not the ends of the blank, but if you mill down to and even slightly into the brass, even directly between centers, you can still have problems.
Hope that helps, or at least gives you an idea of what else to look at.
