Hello,
>
> My understanding is that you have only one key, the traditional rsa key.

This is indeed the case.

> I have tried to reproduce your issue with a fake user on my box: it works 
> here.
> Have you tried to start an ssh-agent by hand ?

Starting ssh-agent by hand with

eval $(ssh-agent)

after login works perfectly fine, and I can add my key with ssh-add,
and it works. ssh

> What is the version of your ssh ? (I am asking because my box is merely a 
> Jessie
> with some Stretch stuff.)


I'm using ssh 1:7.2p2-5

> Can you show your /etc/pam.d/common-session and /etc/pam.d/common-auth and 
> /etc/pam.d/login
> configuration files ?

====> common-session:

#
# /etc/pam.d/common-session - session-related modules common to all services
#
# This file is included from other service-specific PAM config files,
# and should contain a list of modules that define tasks to be performed
# at the start and end of sessions of *any* kind (both interactive and
# non-interactive).
#
# As of pam 1.0.1-6, this file is managed by pam-auth-update by default.
# To take advantage of this, it is recommended that you configure any
# local modules either before or after the default block, and use
# pam-auth-update to manage selection of other modules. See
# pam-auth-update(8) for details.

# here are the per-package modules (the "Primary" block)
session [default=1] pam_permit.so
# here's the fallback if no module succeeds
session requisite pam_deny.so
# prime the stack with a positive return value if there isn't one already;
# this avoids us returning an error just because nothing sets a success code
# since the modules above will each just jump around
session required pam_permit.so
# and here are more per-package modules (the "Additional" block)
session optional pam_krb5.so minimum_uid=1000
session required pam_unix.so
session optional pam_winbind.so
session optional pam_ssh.so debug
session optional pam_tmpdir.so
session optional pam_systemd.so
session optional pam_ecryptfs.so unwrap
session optional pam_ck_connector.so nox11
# end of pam-auth-update config

=======> common-auth:

#
# /etc/pam.d/common-auth - authentication settings common to all services
#
# This file is included from other service-specific PAM config files,
# and should contain a list of the authentication modules that define
# the central authentication scheme for use on the system
# (e.g., /etc/shadow, LDAP, Kerberos, etc.). The default is to use the
# traditional Unix authentication mechanisms.
#
# As of pam 1.0.1-6, this file is managed by pam-auth-update by default.
# To take advantage of this, it is recommended that you configure any
# local modules either before or after the default block, and use
# pam-auth-update to manage selection of other modules. See
# pam-auth-update(8) for details.

# here are the per-package modules (the "Primary" block)
auth [success=3 default=ignore] pam_krb5.so minimum_uid=1000
auth [success=2 default=ignore] pam_unix.so nullok_secure try_first_pass
auth [success=1 default=ignore] pam_winbind.so krb5_auth
krb5_ccache_type=FILE cached_login try_first_pass
# here's the fallback if no module succeeds
auth requisite pam_deny.so
# prime the stack with a positive return value if there isn't one already;
# this avoids us returning an error just because nothing sets a success code
# since the modules above will each just jump around
auth required pam_permit.so
# and here are more per-package modules (the "Additional" block)
auth optional pam_ssh.so use_first_pass debug
auth optional pam_ecryptfs.so unwrap
auth optional pam_cap.so
# end of pam-auth-update config

=====> login:


#
# The PAM configuration file for the Shadow `login' service
#

# Enforce a minimal delay in case of failure (in microseconds).
# (Replaces the `FAIL_DELAY' setting from login.defs)
# Note that other modules may require another minimal delay. (for example,
# to disable any delay, you should add the nodelay option to pam_unix)
auth       optional   pam_faildelay.so  delay=3000000

# Outputs an issue file prior to each login prompt (Replaces the
# ISSUE_FILE option from login.defs). Uncomment for use
# auth       required   pam_issue.so issue=/etc/issue

# Disallows root logins except on tty's listed in /etc/securetty
# (Replaces the `CONSOLE' setting from login.defs)
#
# With the default control of this module:
#   [success=ok new_authtok_reqd=ok ignore=ignore user_unknown=bad default=die]
# root will not be prompted for a password on insecure lines.
# if an invalid username is entered, a password is prompted (but login
# will eventually be rejected)
#
# You can change it to a "requisite" module if you think root may mis-type
# her login and should not be prompted for a password in that case. But
# this will leave the system as vulnerable to user enumeration attacks.
#
# You can change it to a "required" module if you think it permits to
# guess valid user names of your system (invalid user names are considered
# as possibly being root on insecure lines), but root passwords may be
# communicated over insecure lines.
auth [success=ok new_authtok_reqd=ok ignore=ignore user_unknown=bad
default=die] pam_securetty.so

# Disallows other than root logins when /etc/nologin exists
# (Replaces the `NOLOGINS_FILE' option from login.defs)
auth       requisite  pam_nologin.so

# SELinux needs to be the first session rule. This ensures that any
# lingering context has been cleared. Without out this it is possible
# that a module could execute code in the wrong domain.
# When the module is present, "required" would be sufficient (When SELinux
# is disabled, this returns success.)
session [success=ok ignore=ignore module_unknown=ignore default=bad]
pam_selinux.so close

# This module parses environment configuration file(s)
# and also allows you to use an extended config
# file /etc/security/pam_env.conf.
#
# parsing /etc/environment needs "readenv=1"
session       required   pam_env.so readenv=1
# locale variables are also kept into /etc/default/locale in etch
# reading this file *in addition to /etc/environment* does not hurt
session       required   pam_env.so readenv=1 envfile=/etc/default/locale

# Standard Un*x authentication.
@include common-auth

# This allows certain extra groups to be granted to a user
# based on things like time of day, tty, service, and user.
# Please edit /etc/security/group.conf to fit your needs
# (Replaces the `CONSOLE_GROUPS' option in login.defs)
auth       optional   pam_group.so

# Uncomment and edit /etc/security/time.conf if you need to set
# time restrainst on logins.
# (Replaces the `PORTTIME_CHECKS_ENAB' option from login.defs
# as well as /etc/porttime)
# account    requisite  pam_time.so

# Uncomment and edit /etc/security/access.conf if you need to
# set access limits.
# (Replaces /etc/login.access file)
# account  required       pam_access.so

# Sets up user limits according to /etc/security/limits.conf
# (Replaces the use of /etc/limits in old login)
session    required   pam_limits.so

# Prints the last login info upon succesful login
# (Replaces the `LASTLOG_ENAB' option from login.defs)
session    optional   pam_lastlog.so

# Prints the message of the day upon succesful login.
# (Replaces the `MOTD_FILE' option in login.defs)
session    optional   pam_exec.so type=open_session stdout /bin/uname -snrvm
session    optional   pam_motd.so

# Prints the status of the user's mailbox upon succesful login
# (Replaces the `MAIL_CHECK_ENAB' option from login.defs).
#
# This also defines the MAIL environment variable
# However, userdel also needs MAIL_DIR and MAIL_FILE variables
# in /etc/login.defs to make sure that removing a user
# also removes the user's mail spool file.
# See comments in /etc/login.defs
session    optional   pam_mail.so standard

# Sets the loginuid process attribute
session    required     pam_loginuid.so

# Standard Un*x account and session
@include common-account
@include common-session
@include common-password

# SELinux needs to intervene at login time to ensure that the process
# starts in the proper default security context. Only sessions which are
# intended to run in the user's context should be run after this.
session [success=ok ignore=ignore module_unknown=ignore default=bad]
pam_selinux.so open
# When the module is present, "required" would be sufficient (When SELinux
# is disabled, this returns success.)


<======

Thanks again for looking into this,

-- 
Giuseppe "Oblomov" Bilotta

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