People have said that this usually happens when the host tampers with the mission.pbo file, which I have done. I have added many things to my server, including DAYZAI Lite, DayZ Mission system, Auto refuel and Auto repair stations, and a custom map. In the server logs, it says that BattlEye server update attempt has failed, and could not connect to the BE Master.
What actually happens, is when I log on the Mission file takes a few minutes to retrieve, and then I get the "Waiting for Server to Start Authentication", and it waits for 30 seconds, then sends me to debug.
I can post my server logs if you want. I've started up a server back in Oct, but the newest update confused me, so I just re-installed everything, including the server.