Ok so I brought all my script over into my PDI. It does the same thing. Where you see it change the comments but what is posted is not correct. If I comment everything out in my script and just do the 3 lines of code it works.

var comment = g_form.getValue('comments');
var newComment = comment.replace("kb_view.do?sys_kb_id", "prism?id=kb_article&sys_id");
 g_form.setValue("comments", newComment);

Seems to be some sort of timing issues. The question now is how do I get around it.