Peter,
I looked a little more into this, and regardless if you comment out the post-processing routines or not, it seems that FM now always writes a dummy javascript when using the SaveAsPDF routines. The script is actually empty, i.e. it identifies the source as coming from FM, and here's the embedded script in the PDF [it does nothing]:
//<Document-Level>
//<ACRO_source>FrameMaker</ACRO_source>
//<ACRO_script>
/*********** belongs to: Document-Level:FrameMaker ***********/
//</ACRO_script>
//</Document-Level>
It seems that your options are limited here. You can't use the SaveAsPDF route and get rid of the script from the FM end of things. So you can either use AcrobatPro to sanitize the document, create a script that will strip out the javascript or talk to your print provide provider to see if they will let the above script pass their pre-flight.
Alternatively, use the print function to create your postscript and then Distiller to create the final print-ready PDF. If you need to create press-ready CMYK & Spot colour output using the print route, then you'll need to use GrafikHuset's (now freebie) PubliPDF to convert FM's RGB postscript output to CMYK+Spot PDFs. Download at:http://design.grafikhuset.dk/index.php/kontakt/downloads/grafikhuset-publi-pdf and more details available at: http://www.grafikhuset.net/PubliPDF/