The bug you've described seems to have been solved in LightDM shipped with Ubuntu 13.04.
In Ubuntu 12.10 I had the same problem but for a different reason. I had an encrypted home dir and
fingerprint-gui doesn't store passwords to accounts but instead provides a
pam module and only checks for a matching fingerprint to allow users to log in. However, to decrypt a home dir one must enter a password, otherwise encryption simply wouldn't make sense. Thus, as long as
ecryptfs doesn't provide a way to use fingerprints instead of passwords, this system won't work.
Combined with the bug you've described this leads for me to the situation where I have to always first scan my fingerprint for it to fail and only then I'm able to enter a password in
As a workaround, I've disabled fingerprint authentication for
LightDM altogether, after all one has to pass this login quite seldom.
This works as follows:
Make a copy of the file
/etc/pam.d/common-auth, name it whatever you want. For simplicity, I will assume that you named it
sudo cp /etc/pam.d/common-auth /etc/pam.d/common-auth-pass-only
Edit the newly created file for example with the command
sudo nano /etc/pam.d/common-auth-pass-only, you will have to remove the line:
auth [success=2 default=ignore] pam_fingerprint-gui.so try_first_identified debug
The exact contents of this line may differ slightly, but the part with
pam_fingerprint-gui.so will be there.
lightdm pam config file for example with the command
sudo nano /etc/pam.d/lightdm. Replace the file name
common-auth in the line
with the name of the newly created file, the line should then look like this:
Remember, this is only a temporary workaround, the command
pam-auth-update won't manage your config for
LightDM any more after these changes were applied.