Data loss: Server world corruption upon upgrade from 1.7.10 to 1.8.x

Several entities are either missing or broken once an upgrade to 1.8.x is attempted: most notably, missing chests, disconnected Nether portals, and broken doors. Note, this report is regarding a world that has been continuously brought forward since day 1 of the multiplayer survival, so has definitely accumulated entities that are years old. However, it was working fine in 1.7.10. (Well, we fixed most of the misdirected chests and broken doors created by older upgrades, anyway .)

How to reproduce.
1. Copy the (pre-conversion) world to a new directory. (500M tar.gz)
2. Start the server using the updated build and navigate around.
3. Notice missing chests, broken doors, un-activated portals (which appear in new positions once activated).

See attached screen shots for before and after pictures.

BTW, no warnings were present in the logs when upgrading. The server output looked normal.