It's late 2018, and this bug, or variations of it, still plague Xubuntu 16.04, and more than likely other flavors of Xenial. I would not be surprised if it exists in 18.04 as well! It's been around in some form since 2009, and Karmic Koala. Has affected Redhat, Debian and Ubuntu. Don't take my word for it, see the public bugtrackers:
And at that bug, you also find listings for the other 3:
In my case, the most obvious symptom was inability to use ssh keys with passphrases. It may affect ones without as well, since the malfunction prevents ssh keys from loading at all! And I had no permissions problems, it was all gnome-keyring. My keys (yes it refused several, for different SSH servers!) permissions were all 600 (rw for owner, nothing for group or other) as stated in many answers about that. So nothing I could change there.
In Xubuntu, there is a way to disable startup items. Usually also possible in Unity/Gnome/KDE, but I don't have those installed, so can't give specific steps. Not sure of other desktops. Rather than disable SSH agent, GPG agent and other items from Gnome that cause this, and other related bugs, I turned off all Gnome startup items. May be overkill or not an option for some, but SSH is back to working flawlessly on the next reboot!
- Open the Whisker Main Menu -> Settings -> Session and Startup.
- Click the Advanced tab, last one on the right.
- Uncheck (turn off) Launch Gnome Services on startup.
- Close and reboot. Logging out may do it too, but reboot should for sure.
Screenshot of GUI described above:
So, since I gave my fix above, I do hope someone will fix it.
Ubuntu has provably failed to squash it for good, since there are lots of tickets for several releases which claim it is fixed, and more that say "regression", it's back.
Debian probably wants to punt (wash their hands of it) because it's not them, upstream is Gnome.
Redhat probably has a fix only available to paying customers. Because, historically, Redhat is the single biggest employer of paid Gnome developers, which is generous at first glance. Until you realize that means they have financial incentive never to put fixes like this into the free versions, to keep selling Redhat subscriptions.
Gnome is probably the ones who can fix it upstream easiest, and then the others can test and package, without writing a line of code themselves. But the tickets I read say the package has languished for years without an official maintainer! And the two people who voluntarily do so now (thank you) are almost as busy designing a replacement. Why not fix a flat tire even if it takes a year (it's been a decade!) instead of reinventing the wheel first?!