Same problem but with the last pcie-1x slot. It works when 1 gpu is plugged in the slot but it wont recognize the the card in that slot when there are 7 other gpu's connected. TRIED EVERYTHING, going to flash BIOS 0808 when I can find it. It happend when i updated the bios and when windows updated to version 1709...
Been and still am there! But at least yours boots mine immediately goes to boot loop. As you mentioned yourself problem is software wise, have you tried reinstalling the windows?
BTW if you found the BIOS version could you provide us with a link? Thnx.