In order to verify the certificate one needs to construct the whole certificate chain to the trusted/root certificate. Thus xmlsec might need to know not only the certificate you was using for signature but also all the other certificates in the chain.
You code looks reasonable. It would help if you can provide the error returned by MSCrypto. This should tell the exact failure reasons (I hope).
BTW, have you tried to verify your signature with xmlsec command line utility?
Aleksey
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