Can't say for sure what the cause is but there is a few things you could try.
You could buy a CED M2 chronograph as they are more accurate.
You could swap to H4831 powder and adjust your powder load accordingly as it is less temp sensitive. Velocity change from cold to hot may indicate the need.
Buy a Redding body die to go with the neck size only die as it will allow resizing and shoulder bumping without touching the neck area.
You could also neck turn the cases to just do a skim to clean them up about 75% of the diameter and make sure you turn all the way to mark the shoulder slightly . This gives more even neck tension and makes the neck sizing operation straighter and easier and bullet seating straighter .
If you buy a Lee collet neck sizer it will allow sizing of neck turned cases as is .
However you will need advice on how to set the die up.
Bushing dies work good with neck turned cases and allow easy adjustment of sized length. What I do is only size 2 /3 of the neck length , leaving an expanded shoulder below that . This never gets sized when using a body die as the body die does not touch any of the neck. This acts as a centering shoulder right through the whole life of the case after the first fire forming.
This effectivly regains the lost diameter of the neck turning in a factory chamber.
With a bellted magnum you may at some stage need this die also as the case can swell above the belt and be hard to size properly . Some need it some don't . Don't buy it untill you have the problem. http://www.larrywillis.com/diebig.jpg