Friendly URLs problem: folders being pre-pended in internal links

I’ve got a problem which seems to be on modx side:

Links are generating incorrect paths such as:

Where a page
/pagename.html

is referenced within

/containername/

MODx is generating links to:

/containername/pagename.html

WHich obviously returns a 404 error.

I’m wondering whether Apache could be causing this problem in any way, in what it passes to MODx?

The Apache config looks like this:

        <Directory /data/vhosts/foo.example.org/docs/trunk>
            AuthName "Development Site"
            AuthType Basic
            AuthUserFile /data/vhosts/auth-common/htuser
            require valid-user

            RewriteBase /
        </Directory>

        RewriteEngine On

        # Fix Apache internal dummy connections from breaking [(site_url)] cache
        #RewriteCond %{HTTP_USER_AGENT} ^.*internal\ dummy\ connection.*$ [NC]
        #RewriteRule .* - [F,L]

        # The Friendly URLs part
        RewriteCond %{DOCUMENT_ROOT}/%{REQUEST_FILENAME} !-f
        RewriteCond %{DOCUMENT_ROOT}/%{REQUEST_FILENAME} !-d
        RewriteRule ^(.*)$ /index.php?q=$1 [L,QSA]

Well, that’s definitely not the configuration provided by or recommended by MODx.