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One of the first things you might want to try is to capture that traffic with Wireshark and view it through an I/O Graph. Depending on which flavor of TCP is running, you might see patterns of throughput that will give you a better sense of what's going on. Some older implementations of TCP overreact to congestion on high-latency links.
Also, it's worth looking at the SYN and SYN/ACK handshake packets on both ends, particularly looking to see what size receive buffers each side is declaring. It could be that one side or the other is using such a small receive buffer that the other side needs to slow down to avoid overflowing the buffer.
