Problem is 99.9% solved
Looks like this might have been a bug in 1.8.3?
Anyway, the problem is almost solved after upgrading to 1.9rc1. 
There remain 2 invalid entries, caused by the README and index.php files.
I have deleted the README file because it is not needed, however I cannot delete index.php, because it is needed to prevent directory browsing. 
My suggestion for a fix would be to exclude all files with a .php extension. And perhaps other extensions, who knows?
;){kind=link}
;){kind=link}