PCIe Switch Doesn't Detect U.2 NVMe

Question

I am trying to get a U.2 NVMe (FIPS 140-2), Gen 2 (1x4) to get detected by our Computer-on-Module (COM) conga-MA7 which is on a COM Express® (COME) 3.0 Type10 form factor. In between I have a PCIe Switch (PEX8718-AB80BI G). I am only using 2 lanes to connect to the PCIe switch and the U.2 NVMe. The NVMe is not being detected but when I try other U.2's (not FIPs 140-2) they work. They link at Gen3 speeds and are also 1x4 and they still manage to negotiate to 2 lanes. I have other downstream components connected to the PCIe switch, which always get detected. I also tested the Memkor NVMe's with a different system that doesn't have a PCIe switch, but the same COM, and it gets detected.

The COM is running Redhat Linux. When I run lspci, all the PCIe components show up including the PCIe Switch and its downstream ports, except of course, the Memkor U.2. Is there any other diagnostics that I can run in the linux terminal?

We performed a high level signal integrity simulation before printing the PCBs. I confirmed that the 12V are ready before the NVMe comes out of reset. Currently PCIe clock and PCIe fundamental reset follows the PCIe standards. I also made sure that the write protect or erase signals are not interfering at boot up.

I was able to use (not very familiar with) the Broadcom PCIe Switch PDE tool, to help debug. I do see that there is some type of uncorrectable error, but it is taking me time to decipher all the registers. Other than that, I have no indicator like an LED or signal.

My question is, the only difference is that the U.2 NVMe is FIPS 140-2, so I am wondering if this could be a potential issue? My second question is, has anyone seen compatibility issues, where no matter what I try, maybe the NVMe will never work with the PCIe switch.