This should be done UNPOWERED! Turn off the power supply or unplug it, then press and hold the start button to drain power from the capacitors on the mobo. Then move the jumper from it's normal position to the jumpered position, and move it back. Connect the power and boot up, it will take you into the BIOS for you to make adjustments, but be aware it will have reset to factory defaults. If the defaults are what you want anyway, simply exit out and boot normally.
I have had a seriously corrupted BIOS before and also had to remove the motherboard battery and allow the board to completely drain of any residual power.
I tried removing the battery and jumping with same issue still coming up. Still only the same 3 PCIE slots work. I have ordered 2 h97 anniversary boards. I hope that this fixes the issue. Will post back next week when boards arrive.