Several pages won't show up with SEO links enabled in Opencart

Whenever I enable SEO in Opencart settings, all pages, articles etc. who have SEO links gets redirected to public_html/index.php (Opencart is installed in public_html/shop/ folder).

Here is .htaaccess from root public_html folder:

Options -Indexes
Options +FollowSymLinks
Options -MultiViews
RewriteEngine On
RewriteBase /
RewriteRule ^teksti/([^./]+)([/]?)$ teksti.php?niceid=$1 [T=application/x-httpd-php,L]
RewriteRule ^clanki/([^./]+)([/]?)$ clankistran.php?niceid=$1 [T=application/x-httpd-php,L]
RewriteCond %{HTTP_HOST} .*www.domain.com
RewriteRule ^$ sportna_prehrana.php [T=application/x-httpd-php,L]

RewriteRule ^stran.php$ sportna_prehrana.php%{QUERY_STRING} [T=application/x-httpd-php,L,R=301]
RewriteRule ^cart.php$ nakup.php%{QUERY_STRING} [T=application/x-httpd-php,L,R=301]

RewriteRule ^xfit/$ xfit/xfit.php
RewriteRule ^forum/$ forum/index.php

#Redirect permanent page_wellness.php xfit/

#RewriteRule ^internet.html$ internet.php?%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^programska_oprema.html$ programska_oprema.php?%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^storitve.html$ teksti.php?act=storitve&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^podjetje.html$ teksti.php?act=opodjetju&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^pogoji.html$ teksti.php?act=pogoji&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^privatnost.html$ teksti.php?act=privatnost&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^stran.html$ stran.php?aktualno=1&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^podjetje/([^./]+).html$ stran.php?nicepod=$1&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+).html$ stran.php?nicecat0=$1&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+)/a/([^./]+).html$ stran.php?nicecat0=$1&niceart=$2&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+)/([^./]+).html$ stran.php?nicecat0=$1&nicecat1=$2&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+)/([^./]+)/a/([^./]+).html$ stran.php?nicecat0=$1&nicecat1=$2&niceart=$3&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+)/([^./]+)/([^./]+).html$ stran.php?nicecat0=$1&nicecat1=$2&nicecat2=$3&%{QUERY_STRING} [T=application/x-httpd-php,L]
#RewriteRule ^([^./]+)/([^./]+)/([^./]+)/a/([^./]+).html$ stran.php?nicecat0=$1&nicecat1=$2&nicecat2=$3&niceart=$4&%{QUERY_STRING} [T=application/x-httpd-php,L]
ErrorDocument 404 /404.php
#DirectoryIndex page_wellness.php
#DirectoryIndex sportna_prehrana.phpRewriteCond %{HTTP_HOST} ^xy.com$ [OR]
DirectoryIndex vstop.php

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^page_wellness.php$ "http\:\/\/www\.xy\.com\/xfit\/" [R=301,L]

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^page_wellness.php/$ "http\:\/\/www\.xy\.com\/xfit\/" [R=301,L]

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^xfit/urednik/$ "http\:\/\/www\.xy\.com\/xfit\/urednik\/index\.php" [R=301,L]

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^xfit/podstrani/$ "http\:\/\/www\.xy\.com\/xfit\/podstrani\/index\.php" [R=301,L]

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^kontakti/$ "http\:\/\/www\.xy\.com\/kontakti\/index\.php" [R=301,L]

RewriteCond %{HTTP_HOST} ^.*$
RewriteRule ^sportno_drustvo\.php$ "http\:\/\/www\.xy\.com\/sdx\/" [R=301,L]

Here is .htaccess from Opencart (public_html/shop/) folder:

# 1.To use URL Alias you need to be running apache with mod_rewrite enabled. 

# 2. In your opencart directory rename htaccess.txt to .htaccess.

# For any support issues please visit: http://www.opencart.com

Options +FollowSymlinks

# Prevent Directoy listing 
Options -Indexes

# Prevent Direct Access to files
<FilesMatch "\.(tpl|ini|log)">
 Order deny,allow
 Deny from all
</FilesMatch>

# SEO URL Settings
RewriteEngine On
DirectoryIndex index.php index.html site-down.php install.php
# If your opencart installation does not run on the main web folder make sure you folder it does run in ie. / becomes /shop/ 
RewriteBase /
RewriteRule ^sitemap.xml$ index.php?route=feed/google_sitemap [L]
RewriteRule ^googlebase.xml$ index.php?route=feed/google_base [L]
RewriteRule ^download/(.*) /index.php?route=error/not_found [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !.*\.(ico|gif|jpg|jpeg|png|js|css)
RewriteRule ^([^?]*) index.php?_route_=$1 [L,QSA]

### Additional Settings that may need to be enabled for some servers 
### Uncomment the commands by removing the # sign in front of it.
### If you get an "Internal Server Error 500" after enabling any of the following settings, restore the # as this means your host doesn't allow that.

# 1. If your cart only allows you to add one item at a time, it is possible register_globals is on. This may work to disable it:
# php_flag register_globals off

# 2. If your cart has magic quotes enabled, This may work to disable it:
# php_flag magic_quotes_gpc Off

# 3. Set max upload file size. Most hosts will limit this and not allow it to be overridden but you can try
# php_value upload_max_filesize 999M

# 4. set max post size. uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value post_max_size 999M

# 5. set max time script can take. uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value max_execution_time 200

# 6. set max time for input to be recieved. Uncomment this line if you have a lot of product options or are getting errors where forms are not saving all fields
# php_value max_input_time 200

# 7. disable open_basedir limitations
# php_admin_value open_basedir none

As you can see, I inserted DirectoryIndex index.php index.html site-down.php install.php into Opencart's .htaccess because otherwise I got 403 error whenever I tried to visit my front-end unless I typed exactly /shop/index.php into URL.

Could anyone please help me out with this?