When I'm lacing a wheel if the spoke can't line up with the nipple while still having some free angular play I start looking to see why. The only time it was an issue it was clearly a case of the elbows not being bent quite far enough for the head in spokes and the "fix" was simply be put a little pressure on the spoke near the flange to increase the angle of the elbow for these spokes. Either from good luck or good planning (yeah, right... ) I've avoided some of the cases of head bind that I've seen written about recently. There was another thread recently that discussed a topic very similar to this one about much the same thing with spokes being too tight or loose in the flange hole.

If nothing else threads like this sure do help to educate us into taking NOTHING for granted and to check into the most innocent looking factors and conditions when it comes to something like a new wheelbuild.