This issue occurs when running more than 1 instance of Arma 3 on one system.
Headless clients always pick a port sequentially +12 from Steam master. So by default Arma 3 is 2302, therefore steam master is 2304. The first Headless client to connect will use port 2316, the 2nd 2328 ect ect. This didn't used to be a problem but now Battleye uses an additional port.
2302 Battleye port = 2306
2312 Battleye port = 2316.
Therefore if a headless client is running on 2302 (default port 2316) then it directly conflicts with Battleye on a server running 2312.