Here's all I do:
$fdf_file="CMS".$focus->caseid.".fdf";
$pdf_file="CMS".$focus->caseid.".pdf";
$fdf_dir=".\\pdfFiles\\";
exec('pdftk cms1500.pdf fill_form '.$fdf_dir.$fdf_file.' output '.$fdf_dir.$pdf_file.' flatten');
exec('del '.$fdf_dir.$fdf_file);
The only way I got it working was to make sure that my PDF form file, pdftk.exe and libiconv2.dll are in the same directory as the file calling these commands (which in my case is index.php in the root directory) and this works like a charm. Where do you have your files located?