No Villagers?

I've noticed this since upgrading to 1.4.5, but all the NPC villages on the map have no villagers in them, they're empty. What can I do about this?

 

Server properties, bukkit.yml and a list of plugins.

 

Server properties:

#Minecraft server properties
#Sat Dec 22 18:47:07 EST 2012
generator-settings=
allow-nether=true
level-name=Aerth
enable-query=false
allow-flight=false
server-port=25565
level-type=Default
enable-rcon=false
level-seed=(removed)
server-ip=
max-build-height=256
spawn-npcs=true
white-list=false
spawn-animals=true
snooper-enabled=false
hardcore=false
texture-pack=
online-mode=true
pvp=false
difficulty=2
server-name=Aerth Server
gamemode=0
max-players=150
spawn-monsters=true
generate-structures=true
view-distance=10
spawn-protection=16
motd=Welcome to the Aerth Minecraft server\!

bukkit.yml:

# This is the main configuration file for Bukkit.
# As you can see, there's actually not that much to configure without any plugins.
# For a reference for any variable inside this file, check out the bukkit wiki at
# http://wiki.bukkit.org/Bukkit.yml
settings:
allow-end: false
warn-on-overload: true
permissions-file: permissions.yml
update-folder: update
ping-packet-limit: 100
use-exact-login-location: false
plugin-profiling: false
connection-throttle: 4000
query-plugins: true
deprecated-verbose: default
shutdown-message: Server closed
spawn-limits:
monsters: 70
animals: 25
water-animals: 5
ambient: 15
ticks-per:
animal-spawns: 400
monster-spawns: 1
autosave: 0
auto-updater:
enabled: false
on-broken:
- warn-console
- warn-ops
on-update:
- warn-console
- warn-ops
preferred-channel: rb
host: dl.bukkit.org
suggest-channels: true
database:
username: bukkit
isolation: SERIALIZABLE
driver: org.sqlite.JDBC
password: walrus
url: jdbc:sqlite:{DIR}{NAME}.db

Plugins:

AntiXRay, CompatNoCheatPlus, dynmap, Essentials, GriefLog, GriefPrevention, Hyperconomy, ItemStay, MCMMO, MineBackup, Multiverse, NoCheatPlus, NoPortals, NoWeather, PermissionsBukkit, RankSuite, ServerLogSaver, SimpleAutoAnnouncer, Vault, Votifier, WorldBorder, WorledEdit, WorldGuard.

 

Can we see your plugins/multiverse/worlds.yml

 

This is the main world in question:

worlds:
Aerth:
seed: (removed)
environment: NORMAL
type: NORMAL
hidden: false
alias:
name: ''
color: WHITE
pvp: false
scale: 1.0
respawnworld: ''
allowweather: true
difficulty: NORMAL
animals:
spawn: true
monsters:
spawn: true
entryfee:
currency: -1
price: 0.0
hunger: true
autoheal: true
adjustspawn: true
portalform: ALL
gamemode: SURVIVAL
keepspawninmemory: true
spawn:
x: 345.5
y: 65.0
z: 226.5
pitch: 0.0
yaw: 0.0
world: Aerth
autoload: true
bedrespawn: true

 

You are probably just missing them as you have spawn caps on them.

animals: 25

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

 

Villagers are considered animals?

I could see that if it only happenedin one village, but it happens at EVERY village on the map.