The server will be going along fine, no matter what is happening, but all of the sudden someone will get a net error and be dced on their client. But they are still present in-game. Once this happens and they reconnect they will see a clone of themselves and even restarting the server does not fix the issue.

Infact, restarting breaks it for everybody. We moved the map to another machine and it magically worked again, but on the one where the issue happened initially, it stays 'broken'.

EDIT:
No, it's not a duplicate. All of our connections were good. /list shows the duplicates AND if the person reconnects during what happens with us they CAN'T move around like normal, they just get kicked again, making s second/third/fourth duplicate. Once they all do leave, the player still cannot play normally. The ONLY fix we have been able to do was change the physical machine the server is running on.