These are scanned PDFs. It seems that both files saved to the synced and a non-synced folder will corrupt. However, not all my files are corrupting. It seems to do it in batches, where files saved at a similar time will come up corrupt.
I could try scanning the images as a jpeg and see if that helps. PDF was just the default scanner setting. It does seem that my program is having a hard time with PDFs. In fact, I used to try to export the files as PDF, but it took way too long.
Thanks for the help, everyone.