I think the problem here is that the upper redstone wire isn't getting a block update when the lower wire is being placed.
I also moved down my snapshot to 15w34d from 15w42a, and the chunks that had newer blocks were gone, but they reappeared with a snapshot update.
In 15w45a, the chunks don't disappear, but now the repeat command block I used is only activating once.
Command: clone ~ ~ ~-1 ~ ~1 ~ ~ ~ ~-2 replace move
Put in repeat command block, and place redstone block on top
I can confirm that it is fixed in 1.13-pre8.