Flattener causing stitching on transparent vectors?

Hi I've been using adobe acrobat and the flattener preview under the advanced>print production menu. Before I flatten it, this is what it looks like.
http://img171.imageshack.us/img171/1906/normalv.jpg
After using the flatterner, on high resolution tranparency settings, This is what I get.
http://img692.imageshack.us/img692/2503/cutp.jpg
The original file was made in Illustrator saved as a pdf 1.4, the box that the stitching happens to is a transparent vector shape.
I have read somewhere in the forums that this may be a result of Acrobat creating atomic areas? And if I turn on smooth line art, this will not appear on the press. However when I reopen the pdf in Illustrator, the shapes are physically split and are actually in 4 pieces, one of them being larger than the other, hence creating that stitched artifact.
How do I remedy this?

Hi Bill,
Thanks for the reply.
Well as I stated in my original post,
Hi I've been using adobe acrobat and the flattener preview under the advanced>print production menu. Before I flatten it, this is what it looks like.
http://img171.imageshack.us/img171/1906/normalv.jpg
After using the flatterner, on high resolution tranparency settings, This is what I get.
http://img692.imageshack.us/img692/2503/cutp.jpg
The original file was made in Illustrator saved as a pdf 1.4, the box that the stitching happens to is a transparent vector shape.
So I'm not sure what I haven't said. I'm don't know how I can even clarify any more: I have a pdf I made in Illustrator, that I opened in Adobe Acrobat Pro 9, and I'm using the Flattener Preview function under the Advanced> Print Production menu..to flatten transparent objects?
regards,
ppk812

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