Pixel shift in PDF after flattening

Hi,
I made this post some time ago in the Illustrator forum, but it's most likely an Acrobat issue. Here's the link. Perhaps it can be picked up or moved here by admins.
http://forums.adobe.com/thread/1383150?tstart=0
Thanks.

My recomendation of layers was intended for Illustrator layers.
Yes, PDF 1.5 will retain the layers
I'm not an expert, but feel compelled to ask -
Why do you want to flatten within pdf? Spend enough time here and you will take note that Adobe recommends keeping transparency live as long as possible - until print
You printed within Acrobat to pdf to 1.3 - Yep, it was going to flatten, yep yep, no surprise.
I was ablo to replicate your steps (using InDesign for live transparency) producing an output with stitching (Export > 1.3) and without (Export > High Quality)
To test Acrobats internal flattening, rather than Print to PDF I used to Preflight Fixup to flatten, compatability 1.3. Stitching lines occured. I don't think you can work around such.

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