I don't think that is the problem. The slots that share/disable each other are the PCIE_x1_1, PCIE_x1_2, PCIE_x1_3 and PCIE_x4_3 slots.
In the bios setting, I have already set the PCIe Operating mode to be x1 for all slots (instead of x4 for PCIE_x4_3)
Furthermore the Broadcom wifi card occupies the PCIE_x1_1 (top slot), and the 2 port Fresco card (PME-4UI) occupies the PCIE_x4_3 slots and they are detected and works properly.
Furthermore, as part of the earlier testing included swapping around the 2 Fresco cards between PCIE_x1_2, PCIE_x1_1 and PCIE_x4_3 slots, which still result in only the 2 port Fresco card (PME-4UI) being detected, not the 4 port Fresco card (PME-4U).
Admittedly I have not tried putting the Fresco cards into the PCIE_8x_2 slot (which shares space with the gpu) as I intend to fit an lsi card card there