Thank you for posting your issue in Intel wired ethernet communities.
Any changes or update on the system prior to encountering the issue? you may want to do additional testing such as forcing the speed to 1Gbps on X540-T1 and Cisco switch port for isolation.
you can also run System support utility on the affected system and share to us the output file.
System support utility - https://downloadcenter.intel.com/download/25293/Intel-System-Support-Utility
problem has occurred since initial installation.
Have uploaded details to the support case.
Based on the logs, you also have an onboard I218-LM network controller, does the login delay also occurs on that connection?
We have new driver package version 21 posted in our download center, you may want to try it out.
You can close this case.
We have determined that the problem was an improper switch configuration.
the Cisco Nexus 3000 switch did not have Portfast turned on.
(for future individuals the correct command is : spanning-tree port type edge)
(And it didn't matter the device, card or port speed of the device connected, always took 50+ seconds to allow traffic flow.)
Thanks for your help.