Currently there is a issue with villages. You can see this easily by going to a village and /time set night. The villagers act as if they don't know it is night time and will not all move inside houses. After further testing it is starting to appear that the issue may be with Village Collections or other related classes. Not only do villagers not move into what should be valid doors at night, they do not breed. This would indicate that they don't know they are near any valid doors, hence the possibility it is a issue with villages themselves.
If you would like further information or a small test world download that recreates this issue easily, please reply.
(Minecraft 1.4.2 - Forge 6.0.1.337)