I have the same problem after installing Windows 8.1 on my Dell Precision M4700. I have tried running the hardware troubleshooter and it always finds the problem and after that the SD card becomes visible. But after reboot I need to run the troubleshooter again.
I have found what happens is that one of the PCIe ports is disabled at boot:
Intel(R) 7 Series/C216 Chipset Family PCI Express Root Port 8 - 1E1E
I now use the Device Manager to enable this and then the card can be worked with. But still it is not persistent. After reboot I have to enable it again.
I guess there must be a way to make this port persistently enabled, but I have not found a way.