Try tapping the collet nut lightly with a ball peen hammer or similar as you tighten the nut. That usually works for me.
If it doesn't work, you can try just barely snugging the collet nut, put the toolholder and tool in your spindle and indicate. Tap the tool around until the runout is gone, take it back out of the spindle and tighten fully.
And the obvious: Be sure there are no chips or rust on any of the angled mating surfaces on the collets, nuts toolholder.