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My question is; are the partitions totally separate?
There are no parts of the HDD or SSD that belongs to both partition A and Partition B....
This is because the fingerprint sensor on the Asus notebooks is not yet supported in the libfprint library. (It's the Elan Microelectronics reader)
See P. Varet has patched the Realtek driver for Ubuntu 13.10: link Ensure you have...
Look at Installation (from site)
/usr/share/xsessions/
directory to see if there are any X sessions available on your Ubuntu:
...
$ ls /usr/share/xsessions/
openbox.desktop