My animals are also despawning all the time too. Horses with saddles and armor tied to a fence post... All foxes even the ones that came from breeding and had picked up an item and the the ones ties up to a fence post. The horses and foxes that were tied up they are gone but the end of the lead is still attached to the fence post. My sheep and even the ones I have dyed despawn. Yesterday 2 of my skeleton horses despawned. Other members of the realm are also loosing named tagged pet and mobs.
I had the same problem in that I couldn't use the portal and if I did make it through the portal the realm would crash. Members got upset when the realm crashes because they would loose items. I now make the parrot sit on the ground and push him through the portal first. When I get through to the other side he is automatically sitting on my shoulder.