Random time outs.

Since I applied bungee to my server players including myself are disconnecting at random times for the reason "Time out". No errors are logged, I currently have the connection-throttle setting at default (4,000) and the bukkit.yml connection-throttle at -1. In bungee the timeout is 30,000.

The server is fine on RAM and CPU usage is minimal, TPS is 19.9/20

Any ideas?