Photos missing after manually sorting them.

After moving photos from camera roll to iTunes image-sync folder, some images will not resync to my phone. I do not use iPhoto. Pictures was taken by the iPhone 4. Help?
I have a folder on my computer where from iTunes Autosync images. I use this to be able to sort my images into folders/albums without using iPhoto. However after doing this not all of the photos taken by the iPhone 4 will resync to the iPhone and I cannot figgure out why.

When you copied them to the flash drive you took them out of iPhoto and into the Finder. The Finder doesn't understand manual sorting.
Here's one (of several) way(s) to do what you want:
Make an Album of the photos, then drag the pics into your preferred order.
Then Photos Menu: Batch Change -> Set Title to Text "John's Birthday", for instance, and tick the box to append a number to each Photo. Now your photos are titled 'John's Birthday 001, John's Birthday 002 ... etc'
Then File -> Export and in the Export dialogue set the Filename to "Use Title"
Sort on Filename in the FInder and you end up with a folder full of images in the same order as the Album in iPhoto.

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