Layered PDF flattened by CS3

We are using a third party repro tool, which uses PDF as it's native format. When these PDFs are opened in Acrobat Professional (or Adobe Reader), the layers are available as created. However, when we open the same file in Illustrator CS3 (13.0.1, Mac or Windows) the artwork is flattened and all the content is linked as a single group.
Has anyone had a similar experience with PDF files - and, more importantly, fixed it?
TIA for any help offered.

If you click on the single group, can you expand it to layers?
Also, in the originator program, are the images embedded to begin with or just linked? This would make a difference when opening in Illustrator too.

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Layers will only appear in a PDF if you save with PDF with at least Acrobat 6 compatibility and turn on the Create Acrobat Layers option.
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There is no way in the InDesign UI for this not to happen.
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Searching the Adobe Forums, Knowledge Base, and even Google has turned up no results. Any idea what the problem may be?
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PDF layers are part of an overall feature known as optional content in PDF and are conceptually very different than Illustrator layers. Since PDF optional content features in general are very much a superset of Illustrator layers (PDFMaker for PowerPoint uses optional content to handle certain slide build features, for example), there would be no easy way for Illustrator to readily pick and choose what optional content features to support and translate. As such, don't expect this to be "rectified" in any way in future Illustrator releases.
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Layered PDF flattened by CS3

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