Failed Core Validation

How to diagnose why XMLSignature.validate is returning "failed core validation"?
JWSDP 2.0 demos GenDetached and Validate work fine. Modified both to function properly with "file:" input rather than "http:", thus inserted calls to SetBaseURI for the JDK bug work around. Modified versions work fine also [with file: input].
Then moved both pieces of code into my application. Unlike GenDetached.java, which simply generates an internal KeyPair, I create a keystore using keytool -genkeypair. Modified the GenDetached code to read the keystore, extract the cert and thus the public key, and separately the private key. Signed with the private key. Transformed a JAXB object and inserted it into an XML file my application creates. Output looks good. But the code imported from Validate.java indicates "failed core validation", though the one and only reference validation status is "true", i.e., successful.
If I run Validate.java on the XML generated by my app, not GenDetached.java, it too indicates "failed core validation". So something must be wrong with the signing process.
How does one go about diagnosing "failed core validation"? The whole process appears to be simple pass/fail, with no explanation or diagnostic available. Thanks.

More information...
Have modified my app to not only transform a JAXB object and an OutputStream object but also a DOM object, see code as follows:
// output the resulting document to a JAXBResult
TransformerFactory tf = TransformerFactory.newInstance();
Transformer trans = tf.newTransformer();
JAXBContext jcs = JAXBContext.newInstance("com.cryptek.jtdi.dim.dmt.jaxb");
JAXBResult jaxbResult = new JAXBResult(jcs);
trans.transform(new DOMSource(doc), jaxbResult);
JAXBElement<SignatureType> jaxbElement = (JAXBElement<SignatureType>)jaxbResult.getResult();
// output the resulting document to stdout
trans.transform(new DOMSource(doc), new StreamResult(new FileOutputStream("signature.xml")));
// output the resulting document to a DOMResult
DOMResult domResult = new DOMResult();
trans.transform(new DOMSource(doc), domResult);
debugLogger.info("dom " + domResult.toString());
DumpNode(domResult.getNode(), 0);
Very curiously, DumpNode is revealing a <SignatureValue> identical to that produced by the JAXB object, i.e., a value which Validate.java rejects for "failed core validation" but approves reference validation.
Here is the log data for the JAXB transform object and the DOM transform object. Note <SignatureValue> in both cases is the same:
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - dom javax.xml.transform.dom.DOMResult@14ce5eb
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#document: null] name #document type 9 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [Signature: null] name Signature type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [SignedInfo: null] name SignedInfo type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [CanonicalizationMethod: null] name CanonicalizationMethod type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [SignatureMethod: null] name SignatureMethod type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [Reference: null] name Reference type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [DigestMethod: null] name DigestMethod type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [DigestValue: null] name DigestValue type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: HNq7BMuL4wdr6g6YJOuS8DlTcDA=] name #text type 3 value HNq7BMuL4wdr6g6YJOuS8DlTcDA=
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [SignatureValue: null] name SignatureValue type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: gdnCqYJAy7z2xFV35trujkinUluBfp5rbif14yfDPrmrYIZCWlekeA==] name #text type 3 value gdnCqYJAy7z2xFV35trujkinUluBfp5rbif14yfDPrmrYIZCWlekeA==
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [KeyInfo: null] name KeyInfo type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [KeyValue: null] name KeyValue type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [DSAKeyValue: null] name DSAKeyValue type 1 value null
2007-07-27 10:00:09,468 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [P: null] name P type 1 value null
2007-07-27 10:00:09,484 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: /KaCzo4Syrom78z3EQ5SbbB4sF7ey80etKII864WF64B81uRpH5t9jQTxeEu0ImbzRMqzVDZkVG9
xD7nN1kuFw==] name #text type 3 value /KaCzo4Syrom78z3EQ5SbbB4sF7ey80etKII864WF64B81uRpH5t9jQTxeEu0ImbzRMqzVDZkVG9
xD7nN1kuFw==
2007-07-27 10:00:09,484 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [Q: null] name Q type 1 value null
2007-07-27 10:00:09,484 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: li7dzDacuo67Jg7mtqEm2TRuOMU=] name #text type 3 value li7dzDacuo67Jg7mtqEm2TRuOMU=
2007-07-27 10:00:09,500 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [G: null] name G type 1 value null
2007-07-27 10:00:09,500 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: Z4Rxsnqc9E7pGknFFH2xqaryRPBaQ01khpMdLRQnG541Awtx/XPaF5Bpsy4pNWMOHCBiNU0Nogps
QW5QvnlMpA==] name #text type 3 value Z4Rxsnqc9E7pGknFFH2xqaryRPBaQ01khpMdLRQnG541Awtx/XPaF5Bpsy4pNWMOHCBiNU0Nogps
QW5QvnlMpA==
2007-07-27 10:00:09,500 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [Y: null] name Y type 1 value null
2007-07-27 10:00:09,500 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - node [#text: MFc9VKzBT0ilHvURWYyFmwhPyCMdzVSqqkLe/SH+Y40vbZmUbyUboJHA/da0ad1CTjQjvCORXDb1
wml6N+/DOQ==] name #text type 3 value MFc9VKzBT0ilHvURWYyFmwhPyCMdzVSqqkLe/SH+Y40vbZmUbyUboJHA/da0ad1CTjQjvCORXDb1
wml6N+/DOQ==
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - id . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - schemaVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v1.0
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - schemaPublicationStatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . Published
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - processingUrgencyIndicator . . . . . . . . . . . . . . . . . . . . . . . . . . false
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.schemaVersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . v1.0
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.schemaPublicationStatus . . . . . . . . . . . . . . . . . . . . . . . Published
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.CanonicalizationMethodType.Algorithm . . . . http://www.w3.org/TR/2001/REC-xml-c14n-20010315#WithComments
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.SignatureMethodType.HMACOutputLength[0] . . .
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.SignatureMethodType.Algorithm . . . . . . . . http://www.w3.org/2000/09/xmldsig#dsa-sha1
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].DigestMethodType.Other[0] .
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].DigestMethodType.Algorithm . http://www.w3.org/2000/09/xmldsig#sha1
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].DigestValue . . . . . . . . HNq7BMuL4wdr6g6YJOuS8DlTcDA=
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].id . . . . . . . . . . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].URI . . . . . . . . . . . . file:/C:/JTDITransport_svn/foo.txt
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignedInfoType.ReferenceType[0].Type . . . . . . . . . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignatureValueType.id . . . . . . . . . . . . . . . . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.SignatureValueType.value . . . . . . . . . . . . . . . . . . gdnCqYJAy7z2xFV35trujkinUluBfp5rbif14yfDPrmrYIZCWlekeA==
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.P . . . . . . . . . /KaCzo4Syrom78z3EQ5SbbB4sF7ey80etKII864WF64B81uRpH5t9jQTxeEu0ImbzRMqzVDZkVG9
xD7nN1kuFw==
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.Q . . . . . . . . . li7dzDacuo67Jg7mtqEm2TRuOMU=
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.G . . . . . . . . . Z4Rxsnqc9E7pGknFFH2xqaryRPBaQ01khpMdLRQnG541Awtx/XPaF5Bpsy4pNWMOHCBiNU0Nogps
QW5QvnlMpA==
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.Y . . . . . . . . . MFc9VKzBT0ilHvURWYyFmwhPyCMdzVSqqkLe/SH+Y40vbZmUbyUboJHA/da0ad1CTjQjvCORXDb1
wml6N+/DOQ==
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.J . . . . . . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.Seed . . . . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.DSAKeyValueType.PgenCounter . . . . null
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.KeyValueType.java.lang.String . .
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.KeyInfoType.java.lang.String . .
2007-07-27 10:00:10,187 [main] INFO com.cryptek.jtdi.dim.dmt.JTDITransportImpl - JtdiData.Signature.id . . . . . . . . . . . . . . . . . . . . . . . . . . . . . null
And here is the OutputStream result. Note <SignatureValue> is NOT the same as the above, and that Validate.java approves these results:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Signature xmlns="http://www.w3.org/2000/09/xmldsig#">
<SignedInfo>
<CanonicalizationMethod Algorithm="http://www.w3.org/TR/2001/REC-xml-c14n-20010315#WithComments"/>
<SignatureMethod Algorithm="http://www.w3.org/2000/09/xmldsig#dsa-sha1"/>
<Reference URI="file:/C:/JTDITransport_svn/foo.txt">
<DigestMethod Algorithm="http://www.w3.org/2000/09/xmldsig#sha1"/>
<DigestValue>HNq7BMuL4wdr6g6YJOuS8DlTcDA=</DigestValue>
</Reference>
</SignedInfo>
<SignatureValue>E/402n/h/7G4z5tU4hq1UoNc5qM5e7KShpKl/E2Rtx20jrPN1rKVdg==</SignatureValue>
<KeyInfo>
<KeyValue>
<DSAKeyValue>
<P>/KaCzo4Syrom78z3EQ5SbbB4sF7ey80etKII864WF64B81uRpH5t9jQTxeEu0ImbzRMqzVDZkVG9xD7nN1kuFw==</P>
<Q>li7dzDacuo67Jg7mtqEm2TRuOMU=</Q>
<G>Z4Rxsnqc9E7pGknFFH2xqaryRPBaQ01khpMdLRQnG541Awtx/XPaF5Bpsy4pNWMOHCBiNU0NogpsQW5QvnlMpA==</G>
<Y>MFc9VKzBT0ilHvURWYyFmwhPyCMdzVSqqkLe/SH+Y40vbZmUbyUboJHA/da0ad1CTjQjvCORXDb1wml6N+/DOQ==</Y>
</DSAKeyValue>
</KeyValue>
</KeyInfo>
</Signature>

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