As long as you are in speck with the load data I would not be concerned about it.
I have found that powder can fill the case differently depending on how it is dispensed. Try letting the powder trickle slowly out of the powder measure, meaning when you drop the charge don't just let it fall but let the handle down at a snails pace. I have found that the powder packs in the case tighter, and changes how high it ends up in the case. If your using a funnel just pour the charge in slow. Also when holding the case with my thumb and index finger, I hold it tight against the drop tube, or funnel and give it a couple of flicks with the middle finger, (Something like knocking the ash off of a cigarette.) and that will help the powder settle. Use of a longer drop tube may also help.
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