Chests disappearing on world upgrade (not just invisible)

Certain chests disappear entirely when a world is upgraded from <1.7.* to 1.8.*

Reproduction steps with specific map:

1. Get map from http://www.fileswap.com/dl/ymM3oBLedw/ (Sea of Flame II by Vechs)
2. Load map in SMP
3. Enable cheats (Open to LAN, etc.)
4. /tp -97 14 47

Results (also see screenshots below):

• On 1.7.x, the glass box has a chest on top of the stone slab full with Magenta Wool.
• On 1.8.x, the chest is missing completely - no hitbox, it is possible to walk through the empty space.

Additional observations:

• Changing the contents of the chest or placing blocks around the chest (in 1.7), and then re-opening the world in 1.8 doesn't change this behaviour.
• Breaking and re-placing the chest in 1.7 makes the chest appear correctly in 1.8

Note to mods: The bug MC-66631 is flagged incorrectly as a duplicate - it is a duplicate of THIS bug, but both bugs are different to MC-65874 which is visual only. This bug makes the chests disappear entirely and irrecoverably.