If that slot looks physically fine, its hardware issue and there are 2 things that could be wrong.
1. broken wires inside motherboard
2. damaged pcie controller in cpu
Without trying another cpu you cant discover what is wrong and your motherboard have only one pcie 16x slot, so while other one looks same, it is only 4x and this will limit your gpu performance. And if you go and read page 28 in manual, there is written that PCI_E4 is only 4x.