Never quite figured it out myself. It seems to appear at random amongst my lot; a snake that produces a perfect clutch for three years at a stretch, can suddenly produce some with patchy calcification.
I've tried adding a vitamin D3+calcium supplement to drinking water from the start of the year, but this has never made any difference - most clutches are fine, the odd one is still patchy.
Some years, I don't have the problem at all; all eggs are perfect, with no change in feeding regime or supplements.
I've given up worrying about it. Patchy/uneven eggs seem to be as successful as the "perfect" ones.
All my breeding females eat adult mice and nothing else, so I don't think a "bad diet" is a factor. If it was genetic, the same snake would produce patchy eggs consistently - this never happens with me.