Do you shoot in raw and jpeg? And do you automatically stack the jpeg/raw photos? If so, I have found that the files that are not visibile in the stack are not recognized by the Adobe Photo Downloader and will be imported again if you are using the same memory card. If you are importing the files to a folder with the date taken, the duplicate files (normally jpegs) will be given a -1 suffix when imported. If that happens to me, I do a search for files with -1 and delete them from the latest batch import (using the Sort by Import batch filter).