SSH connection to Ubuntu open SSH-server requires

Heyho,

I have a kind of weird problem with an ubuntu server that runs open ssh-server.

Everything configuration wise is working except for one thing. I cannot connect via putty with my .ppk key to the server, right after it booted. I get a "server refused our key". Since the thing is currently running in Virtual Box I still have access over the direct login. So I login with my user and my password and instantly log out again.

Now I can connect via putty and the .ook key. And I have no Idea why. Either I missed some explanation somewhere or I screwed up something somewhere with the configs. If anybody can point me in the right direction I'd be grateful!

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 no

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

# Logging
SyslogFacility AUTH
LogLevel INFO

# Authentication:
LoginGraceTime 120
PermitRootLogin no
StrictModes no

RSAAuthentication yes
#PubkeyAuthentication yes
AuthorizedKeysFile      .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 no

# 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 yes

#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 no

AllowTcpForwarding yes

The key is in the decribed place and everything, and as said, I can connect just fine after logging in directly on the VM after a reboot, but no matter what I try I cannot get it to connect without that one login.

This has been answered many times and is more suitable for AskUbuntu.

In short, you have encrypted home folder (even with your AuthorizedKeysFile) and therefore the server can't authenticate you. One possibility is to move the authorized keys somewhere else (AuthorizedKeysFile /etc/ssh/%u/authorized_keys) and decrypt your home folder upon login or just remove the encryption. Official documentation describes it well.