Snipershot,
There was a fairly long thread here about a year or more ago about how to true up your headstock by boring the jaws ever so little. IIRC the problem was that with a scroll chuck, the truing is only going to be repeatable at the diameter that you originally bored the jaws at. So I like to bore mine at around .625" - 650" as that is right in between the final diameters of tips and joints. My assumption is that the inaccuracy in the chuck is linear, meaning that it gets greater as you move farther away from the original bore diameter.
Tony@Russell Cues- is that your experience or does your runout hold true through the entire range on your chuck?
Neil (Conetip) - I remember your post, but I didn't quite understand it at the time. I'll have to go search and read it again.
Finally, before you bore anything, get yourself a known straight rod, chuck it up and measure the runout along the length of the rod. If it is off, you're going to have to try to determine if it is because the jaws are out or the headstock is not true to the ways. This is tricky to differentiate. But if the headstock is not true, then boring will simply bore a cone in your jaws and not a cylinder.
Sorry for the rambling post.
My 2 cents (based on my experience),
Gary