I was using an fread call, and for some reason it wasn't always returning the correct file size and so chopping off the last bit of the character. Switched to fgets instead.
Life is grand.
Very weird and very frustrating. I should add more, but I'm tired of coding. It's now slated to be a character generator and solo game. Hence this means you now have to log in and create a user account, and then it uses sessions to keep track of you. Now to add sessions and session variables.