I learned that my problem was SmartFTP, I have used this program forever and I set my file types manually to ensure ascii for the right files. It turns out that after it expires (even though you can still use it) it uploads all ascii files in binary, like Navaho suggested. I even watched the upload and it said it was uploading in ascii. Pretty messed up thing to do, why not just disable it when it expires? I am using wsftp now and now having any problems.
