For a conventional cross-lace pattern, I install all of one side's heads-out spokes into alternate holes in the flange and bring these out to nipples installed at every fourth hole on the rim, making sure to use rim holes appropriate to that side of the wheel. (Most -- but not all -- are drilled in a zig-zag pattern.) Next I install the first heads-in spoke for that side and pull is across the opposing spokes so that it crosses over 2, 3, or 4 of them, depending on the pattern I am building. I cross under the last spoke, over all of the others, and I wind the hub appropriately. I then do the heads-out spokes on the other flange, being careful to match the positions on the first side. Your problem may be here -- look through the hub and identify two adjacent spokes, one from each hub flange. These must be parallel. If not, you are winding the spokes more on one side than on the other, which could give you the difference in cross point you note.