I don't know if this changes things but when I had this problem it came from a zombie villager that originally spawned from a spawner in a dungeon. Basically I ventured far and wide for a village with no luck, so I went searching for zombie villagers to cure. I finally found one from a zombie spawner, led him all the way back up to my base on the surface, and trapped him in a small walled off area that he could not escape from and cured him (I stayed for the 3 minutes until he became a villager.) Then I left to go build an underground railroad from my newly built village spawner to my base, and it was quite far away so I may have left the chunk. When I finished the railroad and came back for the villager, he had despawned.
In 1.7.2 I would be placed 4 blocks up and 4 blocks left from the minecart, which led to my death quite a few times. But I just tested the new snapshot (13w48b), and it seems to be fixed.