Apps unable to see files

I seem to be having an issue with my Touch with programs seeing the files that are associated with them. For example, my PDF reader couldn't see the PDFs i had on the device, I had to use iFile to get them to be recognized. I also downloaded My Secret Folder, and i'm testing it, and it sees my photos, but not my videos for some reason. I tried other apps and they can't see them either, even though when i go into the Apple app Videos, they're all there. So i don't understand why it's not working. Any ideas?