Someone asked this question at the beekeeping conference I was just at this weekend, about why his bees would be building from the bottom up and now I cannot rememeber exactly what the experts told him to do to fix it.
the issue here is clustering. wax production requires heat, which requires a cluster. if the bees are in 1 box, and a foundationless box is added above, the cluster will tend to extend up from the established comb (so that they can keep working and caring for the brood). If there are enough bees and it is warm enough, they might also cluster at the top of the new box, but i wouldn't bet on it. the comb that gets built up from the bottom bars will flop over under their own weight before they reach the top bars.
the "fix" is to either put the box on the bottom, or (what we do), is to put 3 or so drawn frames in the middle of the upper box, and put the 3 foundationless frames near the sides of the bottom box. the bees like to be able to climb between combs. if there are enough bees, you can move brood frames, which the bees will definitely try to cluster around (if there aren't enough bees or the weather is too cold, you will likely lose some brood doing this). once the bees are using this central area of comb, the cluster will start to draw comb adjacent to them.
the point is, the bees need to be able to build comb in a cluster, and an empty box on top means that they will have to cluster in more than one place...moving frames up makes it easer for them to do this, and also motivates them to do so.