Why does "-webkit-transform-style: preserve-3d;" make some divs disappear?
I think the problem here is similar to the well-known behavior where position: absolute / fixed div's that don't have a defined height / width can often disappear. In your case, the 3d canvas is looking for <div class="div1"> to have a width defined on it, otherwise it just floats aimlessly in space because you gave it properties that make use of the 3d canvas and I believe that in some indirect way causes it not to expand to contain the child divs.
In any case, you can see that defining height and width on the element with preserve-3d fixes the issue in the JS fiddle: http://jsfiddle.net/nY9v6/