Для использования в Apache-2.4.7 (Ubuntu-14.04) сгенерировал SSL-сертификат от Let's encrypt для основного домена и поддомена через команду

# ./certbot-auto --apache -d mydomain.org -d www.mydomain.org

При этом проверка на https://www.ssllabs.com/ успешна для обоих доменов.

Проблема в том, что нормальный HTTPS контент (с зеленым замком в Firefox) отображается только по адресу https://www.mydomain.org.

При открытии https://mydomain.org в браузере варнинг с желтым значком и словами:
"Незащищённое соединение. Части этой страницы (такие как изображения) не защищены."

И отображается только текст без фона и картинок.

Был автоматически сгенерирован конфиг в /etc/apache2/sites-available с таким контентом:
<IfModule mod_ssl.c>                                                                                                                  
<VirtualHost *:443>                                                                                                                  
ServerName mydomain.org                                                                                                                
ServerAlias www.mydomain.org                                                                                                          
DocumentRoot /var/www/html/mydomain.org/forum                                                                                          

<Directory /var/www/mydomain.org/forum>                                                                                                
        AllowOverride All                                                                                                            
</Directory>                                                                                                                          
SSLCertificateFile /etc/letsencrypt/live/mydomain.org-0001/cert.pem                                                                    
SSLCertificateKeyFile /etc/letsencrypt/live/mydomain.org-0001/privkey.pem                                                              
SSLCertificateChainFile /etc/letsencrypt/live/mydomain.org-0001/chain.pem

Include /etc/letsencrypt/options-ssl-apache.conf                                                                                      
                                                                                                                                      
Header always set Strict-Transport-Security "max-age=31536000; includeSubDomains; preload"                                            
Header set X-Frame-Options "SAMEORIGIN"    
Header set X-Content-Type-Options "nosniff"

</VirtualHost>
</IfModule>
                                                        
остальные конфиги я поотключал:
$ sudo a2dissite 000-default.conf
и
$ sudo a2dissite default-ssl.conf

содержимое /etc/letsencrypt/options-ssl-apache.conf:
SSLEngine on

SSLProtocol             all -SSLv2 -SSLv3                                                                                            
                                                                                                                                      
SSLCipherSuite          ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-AES256-GCM-S
HA384:DHE-RSA-AES128-GCM-SHA256:DHE-DSS-AES128-GCM-SHA256:kEDH+AESGCM:ECDHE-RSA-AES128-SHA256:ECDHE-ECDSA-AES128-SHA256:ECDHE-RSA-AES1
28-SHA:ECDHE-ECDSA-AES128-SHA:ECDHE-RSA-AES256-SHA384:ECDHE-ECDSA-AES256-SHA384:ECDHE-RSA-AES256-SHA:ECDHE-ECDSA-AES256-SHA:DHE-RSA-AE
S128-SHA256:DHE-RSA-AES128-SHA:DHE-DSS-AES128-SHA256:DHE-RSA-AES256-SHA256:DHE-DSS-AES256-SHA:DHE-RSA-AES256-SHA:AES128-GCM-SHA256:AES
256-GCM-SHA384:AES128-SHA256:AES256-SHA256:AES128-SHA:AES256-SHA:AES:CAMELLIA:DES-CBC3-SHA:!aNULL:!eNULL:!EXPORT:!DES:!RC4:!MD5:!PSK:!
aECDH:!EDH-DSS-DES-CBC3-SHA:!EDH-RSA-DES-CBC3-SHA:!KRB5-DES-CBC3-SHA                                                                  
                                                                                                                                      
SSLHonorCipherOrder     on                                                                                                            
SSLCompression          off                                                                                                          
                                                                                                                                      
SSLOptions +StrictRequire                                                                                                            
                                                                                                                                      
LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-agent}i\"" vhost_combined                                              
LogFormat "%v %h %l %u %t \"%r\" %>s %b" vhost_common                                                                                
                                                                                                                                      
CustomLog /var/log/apache2/access.log vhost_combined                                                                                  
LogLevel info ssl:debug                                
ErrorLog /var/log/apache2/error.log

Header edit Set-Cookie (?i)^(.*)(;\s*secure)??((\s*;)?(.*)) "$1; Secure$3$4"

В /var/log/apache2/error.log
[Tue Feb 14 13:30:24.236704 2017] [ssl:info] [pid 5774] [client 178.210.xx.xx:44392] AH01964: Connection to child 2 established (server www.mydomain.org:443)

[Tue Feb 14 13:30:24.238477 2017] [ssl:info] [pid 5021] [client 178.210.xx.xx:44394] AH01964: Connection to child 6 established (server www.mydomain.org:443)

[Tue Feb 14 13:30:28.662109 2017] [ssl:info] [pid 4990] (70007)The timeout specified has expired: [client 178.210.xx.xx:44382] AH01991: SSL input filter read failed.

[Tue Feb 14 13:30:30.056587 2017] [ssl:info] [pid 4986] [client ::1:33442] AH01998: Connection closed to child 0 with abortive shutdown (server www.mydomain.org:443)