Sven Auhagen reported the same issue with Intel NIC attached to
mini-PCIe slots on a custom Armada 8K design.

O.K. so that suggests the issue is on the Armada side.
 

How would you suggest to investigate this issue?

I presume reboot works O.K? So it is possible to toggle the reset
multiple times, but reboot must do something additional which makes it
work? Do you have sources for the bootloader?

Are there status bits in the comphy about the state of the link? Maybe
comphy needs to be kicked to reestablish the link?

       Andrew

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