One other thing to consider is how you're transferring these files. If it's by FTP, then FTP's ASCII and Binary modes do this sort of thing for you. My guess is that you're using it to upload the files to the server, but not to download them, or at least the mode is set incorrectly on the download.

This is the part that's concerning me the most. I'm sure that's where it's being done. I'm just using CuteFTP to upload and download files. I create everything and store everything on my own machine, then upload it to the server.

In some instances, I've needed to edit the file on the server instead of the one on my machine, or the one on my machine has been lost for whatever reason. Sometimes I get this problem I'm talking about. Other times the file looks normal. I'm not sure what the reason is.