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So if I understand your problem correctly, when only serving incoming connections, the server is doing great. Once you start initiating outgoing connections pulling in data from the outside, you see a lot of TCP retransmissions?

If so, I suspect a duplex mismatch or maybe a dirty fiber that is causing packet loss only on the receiving side (from the servers perspective). Loss of ACK packets usually does not introduce many problems, so that could be the reason you were not experiencing any problems before.

How is this server connected? Do you have multiple servers in the same network segment? And if so, is this the only one having these problems?