Incorrect values for SSH_AGENT_PID and SSH_AUTH_SOCK

I have just upgraded to Ubuntu 15.10 and realized when I tried to log in that my ssh private key password is requested in terminal instead of a popup window.

After checking I saw that the related environment variables have values similar to this:
SSH_AGENT_PID=1758
SSH_AUTH_SOCK=/tmp/ssh-q8UkJJDzaYfg/agent.1694

Instead of
SSH_AGENT_PID=1678
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh

It seems that after the upgrade these variables started to have the values belonging to
/usr/bin/ssh-agent /usr/bin/im-launch /usr/lib/gnome-flashback/gnome-flashback-metacity
instead of the ones belonging to
/usr/bin/gnome-keyring-daemon --daemonize --login

The strange thing is that when I realized this I restarted my computer and after that the variables had the right values.
Although I restarted my desktop several times since then and was not able to reproduce the "good" behavior.

So I would expect to have the values belonging to gnome-keyring in those environment variables instead of the ones I currently have as gnome-keyring automatically asks for password and adds ssh keys and the simple agent doesn't.

ProblemType: Bug
DistroRelease: Ubuntu 15.10
Package: gnome-flashback 3.17.2-2ubuntu1
ProcVersionSignature: Ubuntu 4.2.0-16.19-generic 4.2.3
Uname: Linux 4.2.0-16-generic x86_64
ApportVersion: 2.19.1-0ubuntu3
Architecture: amd64
CurrentDesktop: GNOME-Flashback:Unity
Date: Sun Oct 25 21:35:05 2015
SourcePackage: gnome-flashback
UpgradeStatus: Upgraded to wily on 2015-10-22 (2 days ago)