The SYS-421GE-TNRT PCIE slots are running through a PLX switch, besides slot 7. Usually the PCIe cannot be detected is because the driver does not support the PLX architecture, it only looks to the devices directly connected to the CPU root port and can't traverse the additional layer the PLX adds.
The SYS-421GE-TRNT3 has all the PCIe slots connected directly to the CPU, it should avoid this issue.