The first Guise XHTML mummifier called document.normalizeDocument(), which worked fine for simple XHTML5 documents. But in documents using the legacy XHTML 1.1 modularized DTD, which loads other DTDs and other entities in turn, document.normalizeDocument() will print an error such as this:
My best guess so far is that the document.normalizeDocument() method tries to resolve some entities, but not using the EntityResolver that was installed in the document builder that parsed the document. There are some notes about setting resource-resolver in DOMConfiguration.
For now, switching to document.normalize() prevents the problem, and may be all we need anyway.