Fixed it. I turned off the "Create Thumbnail" feature. I didn't think it would still try to generate them if they were already there, but it does.
Just to note... I was uploading my own thumbs because the generated thumbs were all greyed out. I believe this to be caused by my shared hosting using an outdated version of Ghostscript which they refused to update to a more recent version which would have taken them less than 5 minutes to do, as I ended up installing the latest version on my local computer to create my own thumbs. GoDaddy is lazy!!
This is the program I used which gives you a 15 day, full-version trial...
http://www.a-pdf.com/faq/any-tool-to-batch-create-thumbnails-from-a-number-of-pdf-files.htm