Orin AGX: PCIe Root port not detected in Custom Carrier Board

Hi, we have a custom carrier board for Jetson AGX Orin.

Out of the 4 fabricated carrier boards, The PCIe Root port (0001:00:00.0 PCI bridge: NVIDIA Corporation Device 229e (rev a1)) of same Orin AGX module is detected in only two boards.
The device tree is same as Orin dev kit with EEPROM disabled.

What can we suspect in the carrier board which is causing Link-up failure of the Orin root port?

DMESG of Orin Module with Working and Non-working Carrier board:
dmesg_nonWorking.txt (65.2 KB)
dmesg_Working.txt (67.3 KB)

Sounds like a hardware issue. Please review the design.

Also try other kind of PCIe cards to see if it is specific to some kind of cards.

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