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Here are the differences:
NIC1: 82541PI controller using PCI 32bit/33MHz interface. Shared by BMC for IPMI based server management.
NIC2: 82566 PHY using GLCI/LCI interface.
So if you want to use one NIC port for both OS data transfer and IPMI server management, use NIC1. If you're not using IPMI server management, either should work. But you may get better performance on NIC2 due to the difference in PCI interface.