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Intended purpose of the computer is to serve as a FTP over TLS server.

HT Bridge report

As you can see, the certificate is valid for:

ftp.zalohovaniburian.cz

I am unsure why FileZilla shows this:

FileZilla warning

Here's very long vsftpd.conf:

# Example config file /etc/vsftpd.conf
#
# The default compiled in settings are fairly paranoid. This sample file
# loosens things up a bit, to make the ftp daemon more usable.
# Please see vsftpd.conf.5 for all compiled in defaults.
#
# READ THIS: This example file is NOT an exhaustive list of vsftpd options.
# Please read the vsftpd.conf.5 manual page to get a full idea of vsftpd's
# capabilities.


allow_writeable_chroot=YES



#
# Run standalone?  vsftpd can run either from an inetd or as a standalone
# daemon started from an initscript.

listen=YES

#
# This directive enables listening on IPv6 sockets. By default, listening
# on the IPv6 "any" address (::) will accept connections from both IPv6
# and IPv4 clients. It is not necessary to listen on *both* IPv4 and IPv6
# sockets. If you want that (perhaps because you want to listen on specific
# addresses) then you must run two copies of vsftpd with two configuration
# files.

listen_ipv6=NO

#
# Allow anonymous FTP? (Disabled by default).

anonymous_enable=NO

#
# Uncomment this to allow local users to log in.

local_enable=YES

#
# Uncomment this to enable any form of FTP write command.

write_enable=YES

#
# Default umask for local users is 077. You may wish to change this to 022,
# if your users expect that (022 is used by most other ftpd's)

local_umask=022

#
# Uncomment this to allow the anonymous FTP user to upload files. This only
# has an effect if the above global write enable is activated. Also, you will
# obviously need to create a directory writable by the FTP user.
#anon_upload_enable=YES
#
# Uncomment this if you want the anonymous FTP user to be able to create
# new directories.
#anon_mkdir_write_enable=YES
#
# Activate directory messages - messages given to remote users when they
# go into a certain directory.
dirmessage_enable=YES
#
# If enabled, vsftpd will display directory listings with the time
# in  your  local  time  zone.  The default is to display GMT. The
# times returned by the MDTM FTP command are also affected by this
# option.
use_localtime=YES
#
# Activate logging of uploads/downloads.
xferlog_enable=YES
#
# Make sure PORT transfer connections originate from port 20 (ftp-data).

connect_from_port_20=YES

#
# If you want, you can arrange for uploaded anonymous files to be owned by
# a different user. Note! Using "root" for uploaded files is not
# recommended!
#chown_uploads=YES
#chown_username=whoever
#
# You may override where the log file goes if you like. The default is shown
# below.
#xferlog_file=/var/log/vsftpd.log
#
# If you want, you can have your log file in standard ftpd xferlog format.
# Note that the default log file location is /var/log/xferlog in this case.
#xferlog_std_format=YES
#
# You may change the default value for timing out an idle session.
#idle_session_timeout=600
#
# You may change the default value for timing out a data connection.
#data_connection_timeout=120
#
# It is recommended that you define on your system a unique user which the
# ftp server can use as a totally isolated and unprivileged user.
#nopriv_user=ftpsecure
#
# Enable this and the server will recognise asynchronous ABOR requests. Not
# recommended for security (the code is non-trivial). Not enabling it,
# however, may confuse older FTP clients.
#async_abor_enable=YES
#
# By default the server will pretend to allow ASCII mode but in fact ignore
# the request. Turn on the below options to have the server actually do ASCII
# mangling on files when in ASCII mode.
# Beware that on some FTP servers, ASCII support allows a denial of service
# attack (DoS) via the command "SIZE /big/file" in ASCII mode. vsftpd
# predicted this attack and has always been safe, reporting the size of the
# raw file.
# ASCII mangling is a horrible feature of the protocol.
#ascii_upload_enable=YES
#ascii_download_enable=YES
#
# You may fully customise the login banner string:
#ftpd_banner=Welcome to blah FTP service.
#
# You may specify a file of disallowed anonymous e-mail addresses. Apparently
# useful for combatting certain DoS attacks.
#deny_email_enable=YES
# (default follows)
#banned_email_file=/etc/vsftpd.banned_emails
#
# You may restrict local users to their home directories.  See the FAQ for
# the possible risks in this before using chroot_local_user or
# chroot_list_enable below.
#chroot_local_user=YES
#
# You may specify an explicit list of local users to chroot() to their home
# directory. If chroot_local_user is YES, then this list becomes a list of
# users to NOT chroot().
# (Warning! chroot'ing can be very dangerous. If using chroot, make sure that
# the user does not have write access to the top level directory within the
# chroot)

chroot_local_user=YES

#chroot_list_enable=YES
# (default follows)
#chroot_list_file=/etc/vsftpd.chroot_list
#
# You may activate the "-R" option to the builtin ls. This is disabled by
# default to avoid remote users being able to cause excessive I/O on large
# sites. However, some broken FTP clients such as "ncftp" and "mirror" assume
# the presence of the "-R" option, so there is a strong case for enabling it.
#ls_recurse_enable=YES
#
# Customization
#
# Some of vsftpd's settings don't fit the filesystem layout by
# default.
#
# This option should be the name of a directory which is empty.  Also, the
# directory should not be writable by the ftp user. This directory is used
# as a secure chroot() jail at times vsftpd does not require filesystem
# access.
secure_chroot_dir=/var/run/vsftpd/empty
#
# This string is the name of the PAM service vsftpd will use.
pam_service_name=vsftpd
#
# This option specifies the location of the RSA certificate to use for SSL
# encrypted connections.

rsa_cert_file=/etc/ssl/certs/ftp-zalohovaniburian-cz.pem
rsa_private_key_file=/etc/ssl/private/ftp-zalohovaniburian-cz.key



# Turn on SSL
ssl_enable=YES

# Allow anonymous users to use secured SSL connections
allow_anon_ssl=YES

# All non-anonymous logins are forced to use a secure SSL connection in order to
# send and receive data on data connections.
force_local_data_ssl=YES

# All non-anonymous logins are forced to use a secure SSL connection in order to send the password.
force_local_logins_ssl=YES

# Permit TLS v1 protocol connections. TLS v1 connections are preferred
ssl_tlsv1=YES

# Permit SSL v2 protocol connections. TLS v1 connections are preferred
ssl_sslv2=NO

# permit SSL v3 protocol connections. TLS v1 connections are preferred
ssl_sslv3=NO

# Disable SSL session reuse (required by WinSCP)
require_ssl_reuse=NO

# Select which SSL ciphers vsftpd will allow for encrypted SSL connections (required by FileZilla)
ssl_ciphers=HIGH




#
# Uncomment this to indicate that vsftpd use a utf8 filesystem.
#utf8_filesystem=YES
3

It seems that this is normal behavior for filezilla client regardless of whether or not the certificate is signed by a CA or the cert is an x509 (self-signed cert - what I used in my ftps setup). It does not matter whether you use filezilla ftp server, vsftpd, or any other ftpd.

Even Digicert's how-to guide shows that window appearing on first connection:

https://www.digicert.com/ssl-certificate-installation-filezilla.htm

1

I also have had this issue about the "wrong cert" with Terena certificates under Digicert and Komodo.

What it happens is that the client often does not know the intermediate certificate to build the chain of trust; less often the root is not known in older devices.

So the server has somehow to be configured to give the complete chain of trust to the client.

In the case of Radius, I build a pem fileconcatenating the host cert+intermediate root+root, and define it as my certficate in the FreeRaius server.

in Apache I give as certificate the host cert and define as CertificateChain a file with the intermediate root+root certificate.

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