I wanted to see whether I can help, so I ran your program, but I got different result. Both prolog and comments are fine.

It is quite reasonable for me to think that this is a version thing. My XML::Twig is 3.14, however the result might also be impacted by things like expat, XML::Parser and Scalar::Util. 

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE web-app PUBLIC  "-//Sun Microsystems, Inc.//DTD Web Applicat
+ion 2.3//E
N" "http://java.sun.com/dtd/web-app_2_3.dtd">

<!-- This is my comment -->

<web-app>




</web-app><web-app>
  <servlet>
    <servlet-name>Authenticate_en_US</servlet-name>
    <jsp-file>/vxml/en_US/type_0/entry/Authenticate.jsp</jsp-file>
    <load-on-startup>2</load-on-startup>
  </servlet>
</web-app>

[download]
3.14

In reply to Re: XML::Twig Mangles XML prolog by pg
in thread XML::Twig Mangles XML prolog by gjeffrey

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