Are you using the Import Photos function in Family Tree Builder?
In order to import ALL the photos in a specific folder, check the box next to the folder name in the left hand directory tree.
In order import SPECIFIC photos from any folder, double click on the folder and then check the individual photos in that folder.
Double clicking on the folder tells the program that you want to choose which photos to upload in that particular folder. If you would like to automatically upload all photos for a certain folder, take care not to double click on the photo, rather mark the box beside the folder name.