You don't need to print to PDF to flatten. Use the export dialog and choose Acrobat 4 compatibility.
Hi Peter thanks for your reply,
the reason I am flattening the document and using the 'print' option is because I have had trouble with my pngs in the document.
Everytime I print i get the 'dreaded white boxes' around my PNGs, I have fixed that problem now tho with a flattner preset
Acrobat 4 compatibility flattens the PDF and you can specify your custom flattener (and don't forget to check the Simulate Overprint box).
With PNGs are often problems, if they are graphics use AI or PDF/X-4, if they are raster images, use PSD or PDF.
Another reason would be http://indesignsecrets.com/eliminating-ydb-yucky-discolored-box-syndrome.php
But never use print for creating PDFs from InDesign.
I had this problem a few days ago and fixed it using the link you posted thanks, however that link recommends using the 'Print' window.
and now @peterspier says not to use it, so I will just have to do a test
The YDB link is discussing a print issue, so it talks about using the print dialog. I suspect that if you export to PDF/X-4 (which doesn't flatten) you won't see the problem in the PDF.