Well...not sure what is going on. I tried to breed them earlier today and it was acting like each stack of 20 was only 1 animal. I could only breed 2 baby cows from 4 stacks of 20 adults. After breeding a baby pig I tried to kill off a few pigs from a stack of 20, and they all died at once and only gave me 1 raw pork, once again acting like the 20 stack was only 1 pig. Same with shearing sheep, I only got 2 wool from a 20 stack of sheep. Last week the sheared sheep would move away from the stack and I could shear the rest of them. Very confusing.New update. The baby cows I bred earlier today stacked as babies correctly. Once they grew up and I tried to breed them again, they split off as they are supposed to do. Looks like things are working correctly.
I am guessing that with the upgrade to 1.12, the system looked at all previous stacks as "only 1 animal" even thou it still says 20x cow above them. The newly bred stacks also are splitting correctly when you kill off one of them.
So I am good.