Structures (witch huts, nether fortresses etc.) don't get saved with the world file

In 13w19a, I was building a spawning pad for Wither Skeletons around 3 cross sections of a Nether Fortress. After an hour or so of preparation, I noticed there had been no Wither Skeleton spawns in the area.

I copied the world, and used MCedit to clear all other spawnable space within 200 blocks of the pad, and when I got back in game, there were still no spawns. I then loaded the world in 1.5.2, and lo and behold, there were both Wither Skeletons and Blazes spawning on the pad in great numbers.

I switched between a few different versions, checking the spawn pad each time, and it seems that the last version they could spawn there was 13w17a.

What I expected to happen was:
Blazes and Wither Skeletons would spawn on pads created in previously generated fortresses.

What actually happened was:
Only Pigmen and the occasional Ghast spawned on the pads.

Steps to reproduce:
1: Find a nether fortress that was generated in 13w17a or earlier.
2: Observe the lack of naturally spawning Blazes and Wither Skeletons.