I've been working recently on a couple of issues with SignedXml not being able to generate XML signatures following certain standards or validate those signatures properly. Well, at the end we sometimes managed to make things work, but we must note that .NET SignedXml class was only designed to adhere to the XMLDSIG spec. It has no knowledge of SAML, SAML 2.0, SOAP or any other higher level XML protocol. If you are using SignedXml for any other protocol other than XMLDSIG, the scenario is not supported.
From SignedXml article in MSDN:
The class is the main class used for XML signing and verification (XMLDSIG) in the .NET Framework. XMLDSIG is a standards-based, interoperable way to sign and verify all or part of an XML document or other data that is addressable from a Uniform Resource Identifier (URI). The .NET Framework XMLDSIG classes implement the World Wide Web Consortium (W3C) specification for XML signing and verification located at http://www.w3.org/TR/xmldsig-core/.
I hope this helps.
Alex (Alejandro Campos Magencio)