Double check the "Skip duplicate" feature in the Settings. If it's unchecked, tick the box and then start the back-up process again.
Oftentimes, the same photos and videos (or document and audio files on ThePhotoStick Plus) can be saved in various places on your hard disk drive. When the "Skip Duplicates" box is checked, it will result in only one copy of that file being copied to ThePhotoStick. If you uncheck this option and ThePhotoStick finds a duplicate file, it will copy the duplicate file to ThePhotoStick and rename it on ThePhotoStick to {filename}_copy-# (example: DSCF0566_copy-1.JPG).
Important NOTE: By design, ThePhotoStick will not remove any files from your computer, including duplicate files. Skipping duplicates means it will result in only one copy of that file being copied to ThePhotoStick.