I also have a fairly new 4400, without the DRO though. I also had problems, The live center was not center. Clean the tapers, insert the dead centers, and check. Now use the dog to hold a piece and turn it between both centers. Then check to see what run out you get. If everything is good, then place your three jaw on the spindle and try another test cut. Check to see how it did. If good then replace the dead center in the tail stock with the live center and try another cut. See what you get. It does not take much to cause this problem.
Another problem could be what are you using to drill the center, If using the drill chuck that can cause you to drill center a bit off also.
Be sure to put oil on the dead centers. and recheck often. .
Also I have had it where I though it was good on the center but as it spins, it smoothed the item out, and became loose. thus when trying to turn, it was deflecting away from my tool, causing this problem.
Note: I have a second set of fresh pointed centers that I use just to check the alignment as I also due some tapers on purpose, Thus Have to put the head stock back and check it.
I have though about ordering an extra tail stock, or finding one on ebay and making a fully adjustable tail stock to fit mine. T
I hope this helps you out.