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
I did try jumping the slot but didn't work for me, maybe I didn't do it properly... will have another go.
Ask him if he is using v1.0 of the board of v2.0, maybe it makes a difference?