You must make sure that along with the:
php_value auto_prepend_file "filename"
directive, you need to specify the:
php_value include_path "/path/to/file"
directive, as well. And, you must make sure that the document you're requesting is invoking PHP on the server (i.e. if your server doesn't use PHP to process ".html" files, then you will not be able to "auto_prepend" anything to files ending in ".html".