Apparent Serialization Problem

[Wellman, Andrew]

All,
I have a service with the following attributes:
 - Generated code with wsdl2java and therefore have a bunch of custom
types
 - Invokes the service call method from the Client Stub
 - A Handler to add a digital signature

My logic for handling the Digital Signature is as follows:
1) Get the DOM
2) Find the Element to Sign, throw error if not present
3) Find any other signature elements, remove if present
4) Sign the Element
5) Canonicalize the document
6) Reparse the envelope and regenerate the message

I am running into trouble at stage 6.  I have tried both creating a new
envelope and serializing with the SOAPEnvelope(InputStream is)
constructor and DeserializationContextImpl.parse() with the same
results; it whacks my namespaces, most notably my Digital Signature
namespace.

Here is what the document looks like after Canonicaliziation:
<soapenv:Envelope
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";>
 <soapenv:Body>
        <Request xmlns="urn:oasis:names:tc:SAML:1.0:protocol"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>
                <Query xmlns="" xsi:nil="true"></Query>
                <SubjectQuery xmlns="" xsi:nil="true"></SubjectQuery>
                <AuthenticationQuery xmlns=""
xsi:nil="true"></AuthenticationQuery>
                <AttributeQuery xmlns=""
xsi:nil="true"></AttributeQuery>
                <AuthorizationDecisionQuery xmlns=""
xsi:nil="true"></AuthorizationDecisionQuery>
                <AssertionArtifact
xmlns="">AAFIaUJz7PYDhw1R9W7C+Mju31QJKRUihv95nETkJzJa4l+LtoabLvAi</Asser
tionArtifact>
        <ds:Signature xmlns:ds="http://www.w3.org/2000/09/xmldsig#";>
                <ds:SignedInfo>
                .... More Signature Elements Here ....
                </ds:SignedInfo>
                </ds:Signature>
        </Request>
  </soapenv:Body>
</soapenv:Envelope>

Here is what the document looks like after Re-parsing:
<soapenv:Envelope
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/";> 
      <soapenv:Body>  
         <Request xmlns="urn:oasis:names:tc:SAML:1.0:protocol"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>      
            <Query xsi:nil="true" xmlns=""/>   
            <SubjectQuery xsi:nil="true" xmlns=""/>   
            <AuthenticationQuery xsi:nil="true" xmlns=""/>   
            <AttributeQuery xsi:nil="true" xmlns=""/>   
            <AuthorizationDecisionQuery xsi:nil="true" xmlns=""/>   
            <AssertionArtifact
xmlns="">AAFIaUJz7PYDhw1R9W7C+Mju31QJKRUihv95nETkJzJa4l+LtoabLvAi</Asser
tionArtifact>  
            <Signature xmlns:ds="http://www.w3.org/2000/09/xmldsig#";>
               <SignedInfo>
               .... More Signature Elements Here ....
               </SignedInfo>
            </Signature>
         </Request> 
      </soapenv:Body>
   </soapenv:Envelope>

I eliminated some elements for brevity, but the document is unchanged
other than the removal of the "ds" namespace.  Then the document blows
up on the server side because the Signature is now associated with the
default namespace, urn:oasis:names:tc:SAML:1.0:protocol.

I am obviously missing a step or configuration when I serialize.  Does
anyone have an idea what I am missing, or even another approach to the
problem?  I have already tried adding a new Mapping to the Envelope and
Adding my typeMappings to my client-config.wsdd with the same results.

Thank you in advance.

AJ