I noticed that Squids were NOT spawning via Spawners/Natural. They would appear with Spawn Eggs or the /mob command. So I started the process of removing plugins to find the culprit. Nothing changed. So I removed every plugin, still didn't spawn. Then I took the spigot.jar and started a brand new server 100% from scratch. I put Essentials on to change a spawner to Squid. Nothing happened. (I threw the plugin in, didn't modify config.) I took the plugin out and flew around a large ocean for about 20 minutes. Sat for another 20, no squids have Spawned. No plugins, default everything.

I was in the range that Squids 'should' have been naturally spawning.