http://jsfiddle.net/bobbyrne01/Lnq5mffs/
HTML ..
<input type="text" id="separator" value="Doesnt\nwork" />
<input type="button" id="button" value="submit" />
javascript ..
document.getElementById('button').onclick = function(){
    alert(document.getElementById('separator').value);
    alert("This\nworks");
};
Output ..
- first dialog:

- second dialog:

 
    