I used to have a problem with my KOBO Aura (now I have a H2O) where my PC would recognize the reader's internal memory but wouldn't properly detect a microSD card inserted into the reader's external memory slot. Within a minute my PC would freeze and need a reboot to come back to life. Without the microSD card inserted everything would be fine, also there would be no problems if I connected the Aura to the PC in safe mode with the microSd card inserted. I remember asking here for advice but nobody was able to help me. In the end I found a solution which was reinstalling the USB Mass Storage Driver ( I have Win 7 64bit but I think there are also versions for Win 8) via a .bat file available
here