There is a very strange bug in Adobe's XML Data Signatures support. If the target of a manifest includes an "Id" element, the correct transform will not run.

<Reference URI="#410">
    <Transforms>
        <Transform Algorithm="http://www.w3.org/2001/10/xml-exc-c14n#WithComments"/>
    </Transforms>
    <DigestMethod Algorithm="http://www.w3.org/2000/09/xmldsig#sha1"/>
    <DigestValue>6LIx9NZKzbyFXC+qOW/n9bo0RS8=</DigestValue>
</Reference>

If I remove the Id attribute from the Data DOM, it works

<Reference URI="">
    <Transforms>
        <Transform Algorithm="http://www.w3.org/2002/06/xmldsig-filter2">
            <XPath Filter="intersect" xmlns="http://www.w3.org/2002/06/xmldsig-filter2" xmlns:dsig="http://www.w3.org/2000/09/xmldsig#">here()/ancestor::dsig:Signature[1]/../../RBM[1]//. | 
here()/ancestor::dsig:Signature[1]/../../RBM[1]//@* | 
here()/ancestor::dsig:Signature[1]/../../RBM[1]//namespace::*</XPath>
        </Transform>
        <Transform Algorithm="http://www.w3.org/2001/10/xml-exc-c14n#WithComments"/>
    </Transforms>
    <DigestMethod Algorithm="http://www.w3.org/2000/09/xmldsig#sha1"/>
    <DigestValue>...</DigestValue>
</Reference>

<signData target="ballot_stub" ref="$data.signatures">
     <manifest>
            <ref>$data.RBM</ref>
     </manifest>
</signData>