The second URL is suspect. Have you tried to remove the first part, like:

<a href='/intern/cgi-bin/folder.cgi?intern/$file'>
[download]

This should give you an absolute URL http://www.lent.ch/intern/cgi-bin/folder.cgi?intern/$file which I suspect is what you need. Take also into consideration mangling $file to escape bad characters that may tamper the final URL.