I've got the app online so that it can be tested and get this issue rolled out.
First, tinker around with the app in firefox or any modern day browser and get a feel for how the save function works.
Then go and test the save function in IE of any version. You'll notice that it's not interpreting newline characters correctly and thus messes up the output immensely.
Once you understand the problem, any help or ideas on how to fix it are quite appreciated. I believe it has something to do with .html() filtering out newlines in IE.
Thanks in advance.