It's a feel thing. Neck tention can vary. And the way you work the press, if your too fast especially on a case with not so much neck tention you can over shoot the mark.
Pretty much the same with the headspace gauge. Also your calipers take a bit of feel to be consistent. The set up when your zero takes the same feel. From memory the attachment is suppose to be on the fixed side of the calipers I think, there is a reason. I haven't used mine for a while.
Also if your not already.... Before you take a final reading turn the case a bit in the gauge/calipers to basicly settle it square. Another possibility of a fired case is the head or shoulder isn't square reflecting the chamber or some condition of the case being fired.
But really this is all just the nature of the beast, you just find ways to get better or deal with it.
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