Entities removed from world unless in mine carts

Villagers, Chickens etc tend to become non entities. Logging in and out doesn't bring them back, restarting the server doesn't bring them back, they seem to just get deleted from the game. The only way I've found to fix this is to restore from backup.

I found that if I put these things in mine carts they don't go away from the game.

Note: they don't become invisible they are just gone from the game only a map restore from back will bring them back from what I can see.