InDesign CS2-generated PDF & feather effect/transparency issues

I am at my wit's end. I received a client's PDF file created to my specs (same ones we've used for 5 years). I am having massive flattened transparency issues. I am currently using Trueflow version 3, a rip which does not support live transparency; therefore, my distiller settings require that transparency be flattened. There are some horrible results that I can't rectify on my end. There is stitching showing (and outputting to the plate!) where she has placed .psd files on some pages. There is also a problem with feathered objects (which are linked photos) - they look just fine in the document but when exported and flattened, there is a white box behind the pictures instead of the soft feathered look.
When I exported her CS2 file using Acrobat 5 instead of 4, the effect is fine, but - my rip kicks it out. When I export to my specs, the PDF has the above print issues --
I want to clarify that I always view print ready PDF files using output and overprint preview -- this is not a preview issue -- it is a definite file & export & resulting print issue.
I would love to be able to assist my client -- this is a rush job. If anyone has encountered this and has a feeling what may be causing it, please let me know -
Also - I do not have any software to correct this issue -
Thanks in advance -

Peter -- I am looking over those articles now. Here is the problem -- we do not print from the application
File > Print, and under Output, choose Composite CMYK, and CHECK the “Simulate Overprint” checkbox. Under Advanced, select your all-raster flattener.
I do not have her entire document -- only a couple of the problem children.
I suppose a workaround would be to (if I had her files) see if I could print as a postscript and distill it to a PDF -- or print to a postscript and send that into Trueflow to see if it will accept it --
However, I did receive a warning that by creating that high res setting with the slider all the way to the left, it would rasterize the whole page --
Now, I can already do that in just one step by opening the PDF in photoshop at a very high resolution and flattening it --
I simply hate having to go that route when we have type on the page too -- I think my issue is a lack of proper equipment -- we don't like to rasterize if we can help it -
Since this job is a rush, I may have no choice but to do that on those pages -
That info is helpful but in reality is a longer way of accomplishing the same thing --

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Has something changed in CS4 that I don't know about? Could it be the multiply blend mode rather than normal?
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You say that all colors are CMYK. Are you absolutely certain that the background (whatever the rectangular shadow-containing "boxes" knock out) is not a spot color? Your problem description would be more easily explicable if it were.
One workaround suggested was to export the file as a JPG or EPS and save as a Photoshop PDF. We did that on one ad that will run Monday, so we'll see. However, that makes the files with photos enormous -- like from 4 mb to 26 mb
This in itself suggests that these folks do not know what they are doing (though I know that's not terribly helpful to you if you need to advertise with them). I must say that given current economic realities in the newspaper business, it's hard to image a paper refusing to cooperate with a paying advertiser - especially one who has been previously bitten - if not by the newspaper's own incompetence, at least by their unwillingness/inability to provide a proof.

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