There are several reasons why you may be getting excessive runout. The most common cause is when using a standard type die with an expander ball on the decapping shaft that is out of alignment with the axis of the die body. Try loosing off the lock nut and let the shaft float. Also, if you are using that type of die, which is the most common, try smoothing the expander ball radius (not the circumference) on the top part of the ball that first enters the resized neck. You can do this by removing the expander, decapping shaft and using a drill and some wet and dry paper.
I use Wilson hand dies with an arbor press for my 6.5 CM and average about .001" runout with unturned necks on Lapua and Peterson brass.
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