I recently had a similar issue (I'm using ElementaryOS), where I had to enter my key's password every time I used it in the terminal. It used to ask me for the password via the GUI and kept that in memory for a while, but this somehow stopped working.
I tried many of the suggestions found by Googling this (eg. adjust deamon config via gconf-settings, checked startup applications, add to .bashrc, install keychain, ..) but to no avail.
I did find this article on Cup of Linux which suggested checking the pam.d settings in /etc/pam.d/. Since my configuration was definitely different as in the article, I search for pam_gnome_keyring and commented all occurences in all files of the lines
auth optional pam_gnome_keyring.so
session optional pam_gnome_keyring.so auto_start
After a reboot / relogin, I was finally asked by the GUI again for the password..
grep before changes:
:~$ grep -r pam_gnome_keyring /etc/pam.d/
/etc/pam.d/common-password:password optional pam_gnome_keyring.so
/etc/pam.d/lightdm-greeter:auth optional pam_gnome_keyring.so
/etc/pam.d/lightdm-greeter:session optional pam_gnome_keyring.so auto_start
/etc/pam.d/lightdm:auth optional pam_gnome_keyring.so
/etc/pam.d/lightdm:session optional pam_gnome_keyring.so auto_start
grep after changes (note the # in the last 4 lines):
:~$ grep -r pam_gnome_keyring /etc/pam.d/
/etc/pam.d/common-password:password optional pam_gnome_keyring.so
/etc/pam.d/lightdm-greeter:#auth optional pam_gnome_keyring.so
/etc/pam.d/lightdm-greeter:#session optional pam_gnome_keyring.so auto_start
/etc/pam.d/lightdm:#auth optional pam_gnome_keyring.so
/etc/pam.d/lightdm:#session optional pam_gnome_keyring.so auto_start