Problem with PDF/X-1a export in illustrator CS6

I have these huge illustrator files containing a mix of text, vector shapes and placed bitmap pictures cropped using clipping masks.
When I used to save as a PDF/X-1a:2001 in Illustrator CS3, the clipping masks were applied and only the visible pixels were included in the resulting files, which is the proper behavior.
In CS6, this flattening/cropping does not happen and the resulting pdf are very big, containing mostly hidden pixels from the clipped-but-still-included bitmap pictures.
What am I doing wrong here?  I'm exporting as a PDF/X-1a:2001 as before... the "Preserve Illustrator Editing Capabilities" option is unchecked and grayed out...
Idea anyone? Is this a bug in the export module?
Thanks!

So after hours of messing around, here is a solution to apply/crop an illustrator clipping mask on raster images when exporting as a pdf:
- Set the transparency of the top layer to anything other than "normal".
- Export as a PDF.
- Done!
What seems to happens is that setting a transparency setting triggers the flattener (accessible in Object > Flatten Transparency) upon pdf export.

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