I had this problem with music files, and the solution was to make sure the combination of NAME and ARTIST fields of each file is different from any other. If I have two versions of the same song by the same artist, I can't get both onto the iPod unless I give one a different Name, such as "Song Title #VER2".
I think the MC <--> iPod synch looks at Name and Artist fields (and maybe Album and Genre?) to identify a file, but not at the actual file name. If two or more files have the same values in these fields, they are treated as duplicates and only one (if that) ends up being used. The file name, file size, and data in other MC fields such as Track don't seem to be considered by the synch process.
By the way, I know this was happening because I watched the Details view during synching. In earlier MC it stopped and showed a list of "duplicates" (this was only semi-helpful due to the nature of the displayed list, but at least it made me aware). Now it seems to list the "duplicates" at the start of the Details list with a status of Duplicate. If I then change the tags so each of the "duplicate" tracks has a unique Name, the next time it is not listed as a duplicate. So, try it again and watch the Details view.
Assuming iPod synching of photos uses the same logic as music files, the solution is to give each a unique Name field value, perhaps the same value used for the file name.