I have a very similar experience on Ubuntu MATE 18.04.

/run/user/1000/keyring/ssh is opened by gnome-keyring-daemon
/run/user/1000/keyring/.ssh is opened by /usr/bin/ssh-agent
$SSH_AUTH_SOCK points to /run/user/1000/keyring/ssh

When I try to open an SSH session to another machine it hangs just after
"SSH2_MSG_NEWKEYS received"

Changing $SSH_AUTH_SOCK to point to /run/user/1000/keyring/.ssh allows
the SSH to complete

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https://bugs.launchpad.net/bugs/1586835

Title:
  ssh-agent fighting gnome-keyring on Ubuntu Gnome 16.04

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