I have this board also and have the exact same problem, the 1st 1x slot works fine but the middle 2 1x slots do not work at all. I've also tried shorting the slot and still no go. 
I found a guy, who is using the same board, here's what he told me: "I use PCIE1_1 and PCIE1_3. PCIE1_1 does not need jumper. PCIE1_3 needs A1B17 jumper" Maybe this helps you