InDesign Adding Shadow/Lines to Transparent PSD & JPG Files?

I'm relatively new to InDesign, but as I've run this issue through an expert friend of mine who could not puzzle it out- I'm coming here.
I have a number of different images, both JPG's & PSD's that have some transparent areas in them. I'm incorporating them into InDesign files using the "place" command, but when I export the InDesign file to PDF a strange sort of drop-shadow looking effect is coming up between the areas that have images and those that were transparent on the JPG & PSD.
The transparent areas on the JPG & PSD's were created by simply deleting areas of a graphic, or by placing a small image onto a larger transparent background. No masks or clipping paths involved.
Thank you for your help!

I recently attended a seminar with Terry White (http://terrywhite.com/techblog/) and asked him about my issue here. He said, and I am paraphrasing here, that the problem is that my image with a transparent background is being processed through a filter (or something) that readies it for the final image- but the image behind it is not going through this transparency process, and that the inconsistency adds weird black shadows and/or halos under some printing situations.
His solution was fairly simple- take the image BEHIND the one with the transparency, and set the transparency of that image to 99%. Its not visible to your eye, but it means that both images will be process through the "filter" and you won't get those weird halos and shadows.
I haven't had the opportunity to play with his solution much- but on first run-through, it seems to be working for me.

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I've been pulling my hair out over this and finally went to my printer to ask if they had insight as to why this is happening. I'll include his reply here but would like to hear your expert opinions too!
When laying out a file in InDesign, I do a lot of overlapping, feather and some drop shadow and always get a colored shadow behind the transparency area when printing out from a pdf. These files are being designed for print, which is what I thought InDesign was created for - as an updated alternative to Quark and Pagemaker? Here is what the printer says:
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Horgycat,
The CMYK/RGB question is actually pretty complex, and depends to a great extent on how the final output is going to be produced.
If the files are destined for a printing press, all RGB elements must be converted to CMYK prior to printing. You have the option of doing that before placing in ID, or during export to PDF, and there are pros and cons to both methods, but if you don't know until the last minute what the print conditions will be, the convert on export path is more flexible.
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But you mentioned that you are doing exhibition panels, which implies to me that they are probably NOT going on a press -- you need to do hundreds, or sometimes even thousands, of copies to make a press cost-effective compared to digital printing. I used to work in a large-format output bureau doing just this kind of work, and we used large inkjet plotters. In this case, mixed RGB and CMYK files are less of an issue since most plotters will handle either, and depending on if they have an internal or external RIP or none at all, you may actually get better color fidelity using RGB as CMYK colors may get converted in the RIP to the RGB values that the plotter understands, and then get converted back a second time to CMYK (CMYKOG or whatever ink combination is used) internally before the ink is sprayed. Only the print provider would be in a position to tell you the correct color space for the equipment.
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Due to the current unavailability of clairvoyants and mind-readers in the forum, we respectfully request you supply sensible, complete details.
BOILERPLATE TEXT:
Note that this is boilerplate text.
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