Hello irvingsp,
Ragnarok Online Server Emulators will regularly ping the assigned MySQL server to prevent connection loss when there are no player in the server. Unfortunately, when this has been "too much", either the Ragnarok Server Emulator or the MySQL will get "bored". The "Players Online Number" inside FluxCP seems to be a kind of cache, or a saved item. When you see that all of the servers are online in FluxCP, it is definitely true because FluxCP pings to your servers. (your.server.ip.address:6900 -> login server, 6121 -> char server, 5121 -> map server).
It is a natural thing to happen (my own experience). If you would like to know about the error thing, you may do:
./athena-start start >> athena.txt 2>&1 &
This will print out everything displayed (when you usually do ./athena-start start) to a file named "athena.txt"
you may download it through WinSCP and see the logs there.
Have a nice day!