I run a multiplayer server called Arglyx that usually uses Bukkit and several plugins, including Runecraft, Grief Prevention, and Dynmap. However, because of the freshness of the 1.6.1 update, none of my plugins are ready. So, right now, I'm running a vanilla 1.6.1 version of the server with a "FLAT" type world. Nothing special, just a giant "plains" biome with villages.

So, naturally my players and I expected to be able to catch farm animals and corral villagers like we've always done. Unfortunately, it seems that when those chunks containing our mobs are unloaded and later reloaded, all passive mobs with one exception have despawned. The only mobs that don't despawn are Tamed Horses that have Items in their Inventory.

They may be despawning while the chunks are still loaded, but that's kind of hard to prove. I've been standing idle staring at this pen for about half an hour now, so maybe not. I had a couple players say they experienced that, but I can't seem to reproduce it.

TL;DR

What I expected to happen was...:
Passive mobs like cows, horses, pigs, villagers, etc. would spawn naturally on the Flat type server map and I or my players could build a fence around them and keep them as my own.

What actually happened was...:
Once I had them penned, within a few minutes they would just disappear, either from the unloading and reloading chunks or some sort of evil magic (read as "something I don't understand"). All except for Tamed Horses that have Items in their Inventory.

Steps to Reproduce:
1. Let some passive mobs spawn.
2. Pen them up so they can't get out.
3. Leave the area and come back (unload and reload the chunks they occupy) and notice how gone they are. As in, not there. Really gone.