Illustrator vs InDesign vs Rip software problems

I have had this type of conflict for some time now.
Maybe since CS3.
It has occured in 2 ways...
But both stemming from InDesign.
If you create a drop shadow in InDesign (I'm not sure what method or the exact details)
Then export the file, PDF or .AI
and re-open it in Illustrator, it still seems fine.
But when you send the file to a RIP software, all shadows are converted to black boxes.
I do not remember the original rip software this has happened on.
But it happened again, late last year at my current job.
On a different rip software.
The only way around it was to turn the file into 1 big .jpg.
2nd situation is where my question / problem is.
I have a multi-pieced image designed in Indesign 5.5
Converted to .pdf
re-opened in Illustrator CS4.
The background has a repeating vector pattern.
In front is a hexagon shaped, 1 color vector image with white text on top.
In front of that, overlapping by some, is a transparent background image.
probably a .psd
Looks perfectly fine.
Until you send it to the RIP software.
The area where the .psd overlaps the vector image drops out completely.
Like some overprint setting.
Is there some Illustrator overprint setting im missing here?
Or is this yet another InDesign / Rip conflict?

This is called the "yucky discolored box syndrome" and also appears as the "dreaded white box syndrome". http://indesignsecrets.com/eliminating-ydb-yucky-discolored-box-syndrome.php
@Silkrooster: Text should be put on top of all other stuff where it won't be affected by transparency flattening. Unless it shouldn't be deliberately layered by other stuff (like sometimes graphical headlines), of course. But that applies no matter what RIP you are using.

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