mjhjmtu

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
`

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.

@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.

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//.Private is mounted on /home/ so maybe the encrypt home folder option is causing this behavior as well.