Alright, i have traced the problem to ATO itself. Basically, I was experiencing a major problem when my players could never see anyone else on the server when they first logged in within 5 chunks of any online player on the server. This applied to some entities in the area as well.
I narrowed it down to ATO 1.3.3 Causing this problem as 1.3.2 works fine and does not produce this bug.
Also, there are no errors in the console when this happens.