Try double checking that PHPDIG_IN_DOMAIN is set to true and LIMIT_TO_DIRECTORY is set to false. The latter should already be false from post two, but maybe it got switched back to true.
Also, in robot_functions.php find:
Code:
$command = PHPDIG_PARSE_PDF.' '.PHPDIG_OPTION_PDF.' '.$tempfile2;
And replace with:
Code:
$command = PHPDIG_PARSE_PDF.' '.PHPDIG_OPTION_PDF.' '.$tempfile2.' 2>&1';
Then try an index of PDFs and see what prints onscreen.