Objects missing when exporting to PDF, but show up when printing to PDF

Hi - I'm working with someone, both of us in InDesign CS4, and she has some documents that cause a few random objects to just go missing when exported to PDF (same on my computer). But when printing to PDF, they show up fine. They also show up fine if we recreate each individual object, but that can end up being a lot of work. She prefers to export to PDF because of quality. I'm drawing a blank on this one!
The attached file shows the issue. The green blocks just don't want to show up when exporting.

Peter -
The links are just the PDFs of the black and white portions and don't really matter too much since they show up fine when exporting or printing to PDF. Our main concern is the green blocks, which are indeed the green areas of the plan you pointed out. They are actually separate objects created directly within InDesign that can be moved and adjusted.
I just updated to 6.0.4 and that didn't help. I wonder if this may be a variant of the bugs I was reading about with master pages and certain things not showing up when creating PDFs or printing (even though none of these things are on the master page)?
Thanks

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Objects missing when exporting to PDF, but show up when printing to PDF

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