I created a new world in 1.1.5 and started building the same sizes of farms and animal pens as I always build - 9x9 blocks with wooden fence around it.

I didn't notice when, but suddenly all my animals was gone. My son's animals hadn't disappear, his pens are about 4x4 blocks.

Later on I hade a named horse with a saddle and armor on it in a 9x9 block pen. After a restart of the game the horse was gone. My son's animals are still there.

I have also noticed an increased despawn of "wild" animals and mobs, where they can stand just a couple of blocks right in front of and despawn.