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@Gavin – Without having access to the original InDesign file it's hard to say what's going wrong…
Just for testing:
did you try to print to PostScript and distill that to PDF via Adobe Distiller (comes with Adobe Acrobat Pro)?
There is a script by Scott Zanelli (PageExporterUtility5.0.1.jsx), that can export your InDesign file page by page.
Afterwards you can put your single page PDFs together through Adobe Acrobat Pro.
Download Scott Zanelli's script at:
InAcrobat Pro 9 see "File/Combine/Merge Files into a single PDF…"
Thanks Laubender, the PostScript method worked nicely. I was using File>Adobe PDF Presets, which is how I've always done it. We are looking to use this same template more and more, so we will use the PostScript method in the future.
@Gavin – the PostScript method is only half the answer.
I suggested it for testing only.
Be aware that you'll loose live transparency through flattening. So, if you have to export to, say, "PDF/X-4" you'll better use individual page output by the mentioned script and stich the PDFs together afterwards (if the printers demand one single PDF with all your pages).