The original article was written on 2011-11-22 about GNOME 3.0. And I need to update for GNOME 3.1x, because gnome-session-properties has gone.
How to fix
This problem is old enough. For Debian, we have at least two bug reports.
In the files /etc/xdg/autostart/gnome-keyring-ssh.desktop and /etc/xdg/autostart/gnome-keyring-gpg.desktop, we have a line something like:
Please edit this line to:
Then, no desktop environment invokes gnome-keyring for ssh and gpg.
I don't know who need such questionable features of gnome-keyring.
Perhaps, the intention would consolidating all secrets under single application (of gnome-keyring), but the situation/coverage of current implementation is too far to achieve this (hypothetical) goal.
Original head paragraph
In the article GnuPG settings, I wrote how I disable GNOME-keyrings for SSH.
It was for GNOME 2. The old days was good, we just disabled GNOME-keyrings interference to SSH and customizing our desktop was easy for GNU and UNIX users.
GNOME keyrings in GNOME 3
It seems that it is more integrated into the desktop. It is difficult to kill it. It would be possible to kill it simply, but then, I can't use, say, wi-fi access (which needs to access "secrets") any more.
We can't use GNOME configuration tool to disable interference by GNOME keyrings any more. It seems that desktop should not have customization these days.
After struggling some ours, I figured out it is GNOME-SESSION-PROPERTIES to disable the interference. Invoking:
and at the tab of "Startup Programs", I removed radio check buttons for "GPG Password Agent" and "SSH Key Agent".
Now, I use gpg-agent for GnuPG Agent and SSH agent with Gnuk Token.