Because I always start right over left (or vice versa, I can't remember), my shoe laces never have that weird vertical orientation. My son, however, always has this problem.
I think it's a generational thing! Parents show their kids how to tie knots, and they always do it from the front, so each generation sees a mirrored version of the way their parents tie knots. So it goes, backs me forth throughput the years...
Just a theory, but I'm sticking to it.