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The throughput graph is using the 'recvCount' and 'sentCount' metrics, which are derived from the 'recv_cnt' and 'send_cnt' Connection metrics. Per the rabbitmqctl manpage, both of those metrics track the number of packets sent and received, not messages.
Thanks for the report! I missed that one. Version 1.0.1 will have the "Throughput - Messages" graph replaced with "Throughput - Packets".