Modified chest inventory reverts

I'm at a loss ...
When I try to modify the inventory of a chest in the nether or end while no player is around, it often reverts to state before modification once I go back to the nether/end. I can verify that the change does persist until the point that I go back to the nether/end. It does not do this all the time, however, and it doesn't seem to happen at all in the main world or multiverse worlds.

I've tried the following:
- call the BlockState.update() method on the chest after changing
- load the chunk the chest is in before modifying
- save the chunk after modifying

None of this seems to work consistently. Is there any other magic I should know about, or is this a legit CraftBukkit bug? This happens with 1.4.7-R1.0 and older versions.

I feel the urge to bump.

EDIT by Moderator: merged posts, please use the edit button instead of double posting.