Found a solution for this. First, IE handles blob saving differently, specifically it uses:
window.navigator.msSaveOrOpenBlob(new Blob([element], {type:"text/plain"}), "filename.txt");`
If you look at the source code for this page, you will see how they do it.
But to get this to work with cross browser support is a pain.. and a the end of the day you will end up with FileSaver.js.
..which is what I ended up using, and works like a charm.