I had this exact same issue. I found a llama, dragged it through an extreme hills biome to get all the way home, only for me to realise it was gone after I had left and returned to my world 2 times as I was working on a building project and therefore wasn't paying much attention to my llama.
My llama was named and was wearing a carpet, and was in a fenced area which it couldn't have escaped.
I have this exact issue as well. It also effects grass growing on grass blocks for me though.
This has happened for me in the past few versions of minecraft also, however I have only just started to loose progress from it