When I got my Droid 3, I took the SD card out of my D2G, transfered everything on it to my computer, reformatted it and transfered back the files and folders I wanted on the new phone. I had a lot of crap on my card that I didn't need. I never had a problem with doubles or triples of anything, but I can't prove that my method is the reason.
Another person posted a similar problem on this forum just a few days ago. The only difference was that there was no SD card involved in his situation.
If I were in your position, I would transfer the contents of the DCIM folder on my SD card to my computer. Then, I'd delete it from the SD card and reinsert the card. I initially did not transfer the DCIM folder back to the card after reformatting it, but I had pictures in that folder that I needed, that were not in the Pictures folder (they were all camera roll pictures). I added that folder after reformatting and after a few days. No duplicates of anything on my phone. Maybe that will work for you.
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