Piwik does not log visitors

Dear all,

I am encountering an issue with my new Piwik setup.
Recently, my 2 small Magento websites were moved to a new server, running Debian Jessie.
During the migration, everything has been updated to the most recent versions, I use Magento, Piwik for Magento 1.1.8 and Piwik 2.16
Previously, I used a separate Piwik install for every website. To me this seems to add unnecessary overhead and maintenance time.
I now installed Piwik in /opt/piwik/ and created a vhost in Apache, pointing /stats to this folder. The same approach I use for Owncloud, but that does not render any issues.
All domains were added as a trusted host to Piwik.
I can access the Piwik admin from all trusted hosts domains, but Piwik does not log any visitors to either one of the websites.
I have checked the right API code and website ID over and over again, so that is not the issue.
Does anybody have an idea about what I might be doing wrong?

I use the following piwik.conf in /etc/apache2/conf-available

# # Piwik - Logs Alias /stats /opt/piwik
Order allow,deny
Allow from all
AllowOverride None
Options Indexes FollowSymLinks
Require all granted

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule .* index.php [L,QSA]