SSH Agent Does not Work After Update

Question

Since I installed regular updates on Ubuntu 18.04, the ssh agent does not work anymore. If I try "ssh r146" (or any other host where my key is an authorized key) it prompts me on command line for the passphrase.

With verbose output it returns:

ssh -v r146
OpenSSH_7.6p1 Ubuntu-4, OpenSSL 1.0.2n  7 Dec 2017
debug1: Reading configuration data /home/reichelt/.ssh/config
debug1: /home/reichelt/.ssh/config line 35: Applying options for r146
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 19: Applying options for *
debug1: Executing proxy command: exec ssh -W 139.18.11.146:22 ilabws
debug1: permanently_drop_suid: 1000
debug1: identity file /home/reichelt/.ssh/id_rsa type 0
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_rsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_dsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_dsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_ecdsa type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_ecdsa-cert type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_ed25519 type -1
debug1: key_load_public: No such file or directory
debug1: identity file /home/reichelt/.ssh/id_ed25519-cert type -1
debug1: Local version string SSH-2.0-OpenSSH_7.6p1 Ubuntu-4
Enter passphrase for key '/home/reichelt/.ssh/id_rsa': 

Which seems fine to me.

The agent seems to be running:

ps -aux | grep ssh
root      1007  0.0  0.0  72296  5676 ?        Ss   10:05   0:00 /usr/sbin/sshd -D
reichelt  4106  0.0  0.0  11304   316 ?        Ss   10:06   0:00 /usr/bin/ssh-agent /usr/bin/im-launch env GNOME_SHELL_SESSION_MODE=ubuntu gnome-session --session=ubuntu
reichelt  6214  0.0  0.0  21536  1088 pts/1    S+   11:00   0:00 grep --color=auto ssh

The same happens if I use other ssh-using tools like scp.

/etc/log/apt/history.log ends with:

Start-Date: 2018-06-05  09:27:56
Commandline: /usr/bin/unattended-upgrade
Upgrade: liblouis-data:amd64 (3.5.0-1, 3.5.0-1ubuntu0.1)
End-Date: 2018-06-05  09:27:57

Start-Date: 2018-06-05  09:28:00
Commandline: /usr/bin/unattended-upgrade
Upgrade: liblouis14:amd64 (3.5.0-1, 3.5.0-1ubuntu0.1)
End-Date: 2018-06-05  09:28:00

Start-Date: 2018-06-05  09:28:04
Commandline: /usr/bin/unattended-upgrade
Upgrade: python3-louis:amd64 (3.5.0-1, 3.5.0-1ubuntu0.1)
End-Date: 2018-06-05  09:28:05

Start-Date: 2018-06-06  01:34:06
Commandline: packagekit role='update-packages'
Upgrade: libpulsedsp:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), pulseaudio:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), libncurses5:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libncurses5:i386 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libpq5:amd64 (10.3-1, 10.4-0ubuntu0.18.04), libncursesw5:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libpulse0:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), libpulse0:i386 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), libtinfo5:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libtinfo5:i386 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libpulse-mainloop-glib0:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), libncurses5-dev:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), libtinfo-dev:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), ncurses-term:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), ncurses-bin:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), ncurses-base:amd64 (6.1-1ubuntu1, 6.1-1ubuntu1.18.04), pulseaudio-module-bluetooth:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1), pulseaudio-utils:amd64 (1:11.1-1ubuntu7, 1:11.1-1ubuntu7.1)
End-Date: 2018-06-06  01:34:12

Start-Date: 2018-06-06  10:06:16
Commandline: /usr/bin/unattended-upgrade
Upgrade: git-man:amd64 (1:2.17.0-1ubuntu1, 1:2.17.1-1ubuntu0.1), git:amd64 (1:2.17.0-1ubuntu1, 1:2.17.1-1ubuntu0.1)
End-Date: 2018-06-06  10:06:23

I assume the update finished at 2018-06-06 01:34:12 made the change, at least it worked yesterday and stopped working today.

Is this a known issue / can I further debug this issue?

EDIT This still happens from time to time. After 3 in 4 boots, I can normaly use the ssh agent and its GUI; in one of 4 boots, I have to add the key manually. Therefore, I assume that there is no relation with the update.