Thanks you both. There was no configuration in the template, so I added the 
suggested lines. Also there was no domain configured, so I configured my 
(sub)domain. After both changes, the menu still linked to the main domain.

There is a .htaccess in the subdomain main folder. Here is the relevant part. I am 
suspecting the "rewritebase", but since the .htaccess file is in the main 
directory I don't know whats wrong?


### Begin: Rewrite stuff ###
# Enable URL rewriting
RewriteEngine On

# To assist in debugging rewriting, you could use these lines
# DON'T enable it for production!
# This will only work in httpd.conf, not in .htaccess files
#RewriteLog /var/log/apache/rewrite.log
#RewriteLogLevel 9

# If you use the RealUrl extension, then you'll have to enable the next line.
# You will have to change this path if your TYPO3 installation is located
# in a subdirectory of the website root.
# # If you place this in httpd.conf, you cannot use this directive in any case!
RewriteBase /

# Rule for versioned static files (see 
$TYPO3_CONF_VARS[BE][versionNumberInFilename])
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.+)\.(\d+)\.(php|js|css|png|jpg|gif|gzip)$ $1.$3 [L]

# Stop rewrite processing if we are in the typo3/ directory
# For httpd.conf, use this line instead of the next one:
# RewriteRule 
^/TYPO3root/(typo3|t3lib|tslib|fileadmin|typo3conf|typo3temp|uploads|showpic\.php|favicon\.ico)/
 - [L]
RewriteRule 
^(typo3|t3lib|tslib|fileadmin|typo3conf|typo3temp|uploads|showpic\.php|favicon\.ico)/
 - [L]

# Redirect htp://mysite/typo3 to htp://mysite/typo3/index_re.php
# and stop the rewrite processing
# For httpd.conf, use this line instead of the next one:
# RewriteRule ^/TYPO3root/typo3$ /TYPO3root/typo3/index.php [L]
RewriteRule ^typo3$ typo3/index_re.php [L]

# If the file/symlink/directory does not exist => Redirect to index.php
# Important note: If you copy/paste this into httpd.conf instead
# of .htaccess you will need to add '%{DOCUMENT_ROOT}' left to each
# '%{REQUEST_FILENAME}' part.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-l

# Main URL rewriting.

# If you use Windows and SimulateStaticDocuments do not work, try adding a
# slash (/) right before 'index.php' below.

# The example shows how to rewrite only *.html and *.pdf files to index.php
# This may be helpful when using an extension that can generate PDF files
# on the fly.
# Example: RewriteRule .*\.(html|pdf)$ index.php [L]

# For httpd.conf, use this line instead of the next one that has no '#':
# RewriteRule .* /TYPO3root/index.php [L]

# For use with the RealUrl extension, you might need to remove the
# RewriteBase directive somewhere above and use this line instead of the
# next one:
RewriteRule .* /index.php [L]

# RewriteRule .* indexTemp.php [L]

### End: Rewrite stuff ###


Thanks in advance for your help.

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