SSH requires password for first login

Question

So I've got a strange issue going on with SSH. I've set up my SSH server to allow passwordless logins via SSH keys. However, when I try to login, the first time I login after a long time (~day), it requires a password. If I immediately close the connection and try to ssh-connect again it accepts the SSH key. Does anyone know how to get this so it always accepts the SSH key?

Here's my /etc/ssh/sshd_config

# Package generated configuration file
# See the sshd_config(5) manpage for details

# What ports, IPs and protocols we listen for
Port 22
# Use these options to restrict which interfaces/protocols sshd will bind to
#ListenAddress ::
#ListenAddress 0.0.0.0
Protocol 2
# HostKeys for protocol version 2
HostKey /etc/ssh/ssh_host_rsa_key
HostKey /etc/ssh/ssh_host_dsa_key
HostKey /etc/ssh/ssh_host_ecdsa_key
HostKey /etc/ssh/ssh_host_ed25519_key
#Privilege Separation is turned on for security
UsePrivilegeSeparation yes

# Lifetime and size of ephemeral version 1 server key
KeyRegenerationInterval 3600
ServerKeyBits 1024

# Logging
SyslogFacility AUTH
LogLevel INFO

# Authentication:
LoginGraceTime 120
PermitRootLogin without-password
StrictModes yes

RSAAuthentication yes
PubkeyAuthentication yes
#AuthorizedKeysFile %h/.ssh/authorized_keys

# Don't read the user's ~/.rhosts and ~/.shosts files
IgnoreRhosts yes
# For this to work you will also need host keys in /etc/ssh_known_hosts
RhostsRSAAuthentication no
# similar for protocol version 2
HostbasedAuthentication no
# Uncomment if you don't trust ~/.ssh/known_hosts for RhostsRSAAuthentication
#IgnoreUserKnownHosts yes

# To enable empty passwords, change to yes (NOT RECOMMENDED)
PermitEmptyPasswords no

# Change to yes to enable challenge-response passwords (beware issues with
# some PAM modules and threads)
ChallengeResponseAuthentication no

# Change to no to disable tunnelled clear text passwords
#PasswordAuthentication yes

# Kerberos options
#KerberosAuthentication no
#KerberosGetAFSToken no
#KerberosOrLocalPasswd yes
#KerberosTicketCleanup yes

# GSSAPI options
#GSSAPIAuthentication no
#GSSAPICleanupCredentials yes

X11Forwarding yes
X11DisplayOffset 10
PrintMotd no
PrintLastLog yes
TCPKeepAlive yes
#UseLogin no

#MaxStartups 10:30:60
#Banner /etc/issue.net

# Allow client to pass locale environment variables
AcceptEnv LANG LC_*

Subsystem sftp /usr/lib/openssh/sftp-server

# Set this to 'yes' to enable PAM authentication, account processing,
# and session processing. If this is enabled, PAM authentication will
# be allowed through the ChallengeResponseAuthentication and
# PasswordAuthentication.  Depending on your PAM configuration,
# PAM authentication via ChallengeResponseAuthentication may bypass
# the setting of "PermitRootLogin without-password".
# If you just want the PAM account and session checks to run without
# PAM authentication, then enable this but set PasswordAuthentication
# and ChallengeResponseAuthentication to 'no'.
UsePAM yes
`

Answer 1

This can happen on systems with auto-mounted home directories, like in a system with Active Directory or LDAP. Type mount after you login to see if your home directory was auto mounted. Unfortunately, there isn't a way (that I know of) to fix this. Usually, an entire /home directory is mounted, so all user's home directories are available during SSH authentication.

Answer 2

@Paul's answer was was great help in finding a possible solution. To fix, you can mount the root directory with --bind and copy your ssh's authorized_keys, as in

mkdir /mnt/root
mount --bind / /mnt/root
cp -a ~/.ssh /mnt/root/user

This mounts the containing file system to /mnt/root, accesses the mount point (you need to replace user with your user name), copies the .ssh folder, so it can be accessed before the encrypted filesystem is mounted.

Answer 3

This happens for me also but my /home partition is not a separate mount. HOWEVER, I did use the encrypt my home folder option when I created the account and I noticed that /home/.encryptfs/<userid>/.Private is mounted on /home/<userid> so maybe the encrypt home folder option is causing this behavior as well.