Breaded animals (babies) are disappearing somehow and rare mob spawning

Hello Mojang and team,

I have been experiencing a problem with my cows and a few other mobs randomly that when I bread them they disappear when I come back to them after I leave the area or log-out, back-in. This has been happening multiple time and at first I thought they were just glitching threw the floor to there death (I had a hug hole under it 1 block as floor), but after a while of this happening I moved 3 cows outside to the surface took wheat breaded them then (I saw the babe) then walled to my roof, went through the nether portal, went through one that connected to the main town (far away) came back look at my cow farm and there were only 3 cows and no babe. This map in particular has had issues because mobs, although on normal difficulty, spawn extremely rare in groups of one, as of 1.4.7; however; the snapshot, 13w07a, has seemed to make them spawn in normal groups and a little more frequently. I don't know if this is a map issue or a computer or even a bug, but I would like to know how to fix it.

Thanks,
Gregory Brown