Jenni Wiedanook
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Not sure if I can confirm this exact error still occuring in 1.7.9 but it's something similar and might be related.
Here is what I know:
I've got two servers running on a virtual server on my root server. They were both version 1.7.5 and I'm using Multicraft to manage the servers.
Two days ago the disconnecting started without apparent reason (no changes have been done to the server). Players were kicked, receiving a "java.io.IOException: A connection was throttled by the remotehost" on their minecraft screen. This happened on both servers and started around the same time.
My console always showed the same thing for every player:
[23:01:02] [Server thread/INFO]: MissPepperpot lost connection: Internal Exception: net.minecraft.util.io.netty.handler.timeout.ReadTimeoutException
Nothing else, just a bunch of those messages for every player that got disconnected. It was the exact same thing for various versions of craftbukkit and spigot on 1.7.2 and 1.7.5. and also with java 7 (update 55) and java 8 (update 5) running on the server.
Now I recently updated to 1.7.9, hoping that it might eliminate the problem. But still, players get kicked from the server. The message on the minecraft screen is still the same. Console output changed though:
[23:07:06] [Server thread/INFO]: MissPepperpot lost connection: Timed out
No more io.netty but the phenomenon is still pretty much the same. All players get disconnected at the same time, the server keeps running but takes a moment before being available again.
The error is still random and I can't fathom how to reproduce it except by waiting for it.
Not sure if this does help you in any way. If you need any further information, please let me know.
Just do add info to what Aaron said about world issues: My two servers run the same world. I use one server for playing and one for plugin tests. The test server is a copy of the main server. But the last time I copied the main server to the test server was weeks, if not months, before the issue occured for the first time. A lot has happened on the main server's world since then while the test server is essentially still the same. And still the error started occuring at the same time on both servers. So if it's a world issue it would take a while to surface.
I'm going to delete the world files on my test server tonight and keep all the other settings to see if it keeps happening with a fresh world.