EDIT: Found it, the textarea was inside mainBody and that was getting replaced by the Loading message.
Change it to this and it worked
Code:
$(".replyer").click(function(event){
event.preventDefault();
var Link = $(this).attr("href");
var Issue = $("#issueBox").val();
var Rel = $(this).attr("rel");
$("#mainBody").html("Loading…");
$.ajax({
type: "POST",
url: "pages/"+Link,
data: Rel+"&issue="+Issue,
success: function(msg){
$("#mainBody").html(msg);
}
});
});