I have the same exact problem running both the Ubuntu 15.04 and Windows 8.1 side of my laptop. The only things visible to me are the $Recycle.bin and System Volume Information folders that Windows automatically creates.
Thanks for your reply!
No! I didn't trye to add the image manually! I did it using Flash Tool Lite.
I thought the image files were in Edison drive. What kind od files should I save into the Edison Drive?
JCarlos, the Intel Edison drive is used to flash the board with the reboot ota method. This method requires you to put the image files in the drive and then from the console you run the reboot ota command to start flashing the device. Once the board is flashed you can delete the files of the drive.