PCIE Device Not Found by Self-built UEFI

We are using a custom Orin AGX for PCIe function. Everything is working fine after system boots up to recognize our PCIE device (or a SSD).

As we need to customize the UEFI for boot logo, we modify the UEFI sources for that and build its binary according to Home · NVIDIA/edk2-nvidia Wiki · GitHub. We are using JetPack 5.1.2 and L4T-35.4.1 so we use the Combo uefi-202308.1for the UEFI source for the build.

The problem is that if we use the original UEFI from JetPack, our PCIE device can get recognized to use after every system boot. However, if we build our UEFI and flash into the system, our PCIE cannot be recognized sometimes. It looks like there are some timing issues with our PCIE device in its bus negotiation process.

To cross check, we build the original UEFI source by uefi-202308 and flash into the system, the same happen. It looks like it is not caused by our modification for the boot logo.

Also, is JetPack 5.1.2 and L4T-35.4.1 using the same UEFI version of uefi-202308 for the pre-built UEFI binary?

Please advice and help for any hints.

Thank you

Sorry for the late response.
Is this still an issue to support? Any result can be shared?