I guess you checked the windows device drivers, and established that the device itself is defect. This must be a pain.
Another way to handle your problem would be to put the concerning files/directories on the external sd and copy them with a script to the internal sd. In the Kobo Start Menu, you can browse the external sd for scripts and execute them ("scripts > external sd > list sh on sd.msh").
The script on the external sd could be something like
copyKoboRoot2internalSd.sh
Code:
cp /mnt/sd/KoboRoot.tgz /mnt/onboard/.kobo/