If you had the files visible in Finder then the issue was nothing to do with iPhoto. OSX isn't as different to Windows as you seem to think it is

If the files wouldn't copy to the flash drive it was due to some the issue stopping the files being written to the drive. Apart from the possible NTFS issue it is hard to know what the problem was without seeing the problem in person.

Even if the files are managed by iPhoto, the originals are still there in plain files on the file system.