Transparency flattening - unwanted color added to transparent PSD files (IDCS3)

Recently (after switching to CS3) I began experiencing frustrating problems in relation to (what I think is the problem) transparency flattening.
The problem seems to evolve in the printing process where "something" messes up the transparency by adding a 1% (typically) magenta color to the transparent flattened image. (I´m using transparent PSD-files)
This means that the bounding box-area of the image is actually visible in print! I can see this on my own prints (tested on several in-house printers), but worse is that I´m having the same problem with the material I receive from the printing house.
- When I check my PSD files in Photoshop there is no color but a transparent background.
- In Indesign I´ve tried a lot of different output settings and job option files but with the same result.
- In Acrobat my "output preview" measures no deviations, but when I (touch up tool > right click) edit image from inside Acrobat and the image file opens up in Photoshop the 1% is added.
For now I´m dealing with the problem by adding clipping paths to my PSD files which is a pretty untenable situation!
Apparently the problems seems to occur also on transparent .tiff filer etc.
I´m working in CS3 on OSX and I haven´t changed my workflow whatsoever since CS2.
The printing house is aware of the problem but haven´t experienced the problem before.

Sounds to me like an RGB/CMYK colour space issue.
If your image is in RGB but your InDesign document export settings are for CMYK (or vice versa) then you have Adobe converting the colours for you. Since there is a colour shift between the two colour spaces, you have no control over how the conversion happens.
In photoshop, "white" is not the same between RGB and CMYK and I often find there is 1 or 2% magenta in the mix (just as you're finding) when going from RGB to CMYK.
The transparency flattener function is pretty much the same as flattening the layers in photoshop - when it gets to the bottom layer you get one image with a box around it. the same in InDesign - everything that has a transparency (including images with no background) is flattened down on all the objects underneath to create a single image. If the transparent object is just on the paper then it gets a white box around it.
I suggest you check that your images are converted to CMYK in photoshop, and that your PDF export settings in InDesign convert all colours to CMYK. then ensure you use the High Quality in the transparency flattener settings.
Good luck!

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