Plug in one card to one of the 16x slots to see if the computer sees it. Now test the other 16x slot with the same card. If both slots work with one video card then most likely it's not a faulty slot on the mobo.
Im using:
ASUS Prime Z270-P
6 x MSI RX 580 8GB Hynix memory
64-bit Windows 7
Board has 4x 1x PCIE and 2x 16x PCIE.
If I plug same card in all 1X PCIE it's working. If I plug in two 16x PCIE, computer doesn't recognise the card.
Is it fault 16X PCIE ports ( faulty motherboard) or is some settings in BIOS ?