Playing single player (vanilla 1.6.4), I left the game running while I went out for approximately 2 hours. Before leaving I put all of my valuables into 2 chests just in case I died. There was a crafting table in between the two chests. I left the game unpaused in an attempt to farm cacti while I was gone.
I left myself parked in the same room as the two chests.
When I came back, both chests, the crafting table, and the ladder that was used to exit the room I was in were all gone. A few of the stone blocks in the same room also seem to have moved. There is a one block hole in the floor that wasn't there, and there is an extra block in a spot on the wall that wasn't there.
I know that I didn't die because I still have everything that was in my inventory. I know that the game time was advancing because I have more cacti and all of my plants grew.
There is no damage to the room I was in that would indicate an explosion and as far as I know it would not have been possible for any mobs to get in.
Every other section of my house is in the exact same state as it was when I left, including my enchanting room which was in the next room over (no door in between)
How could my chests, a crafting table, and a ladder simply vanish over the course of 2 hours while I left the game running?
I tried using task manager to kill the game and re-launch it but that made no difference.