According to the theory (I first heard if from Precision Rifle, but it makes sense), occasionally the power of the 209 ignition will unseat the bullet/sabot combo before the powder charge actually ignites. The inconsistency in pressure and position of bullet at time of ignition causes a significant shift in impact, ie a "flyer" from an otherwise tight group. Think of it this way...if you measured your barrel and stopped ramming the bullet when it was 1-2" off the powder charge, do you think it would fly the same as a properly seated bullet? (OF COURSE, DON'T TRY THIS!!!). Bullet seating pressure can affect accuracy, so imagine what would happen if the bullet is actually UNseated.
That's the theory. I have personal experience to back it up. But it's still a theory all the same. Like I said, if the gun shoots fine I won't bother with it. But on my old gun it caused me to switch back to the #11 cap to get rid of flyers.