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Signature Validation issue for different java version(ie 1.6 and 1.8)

Signature Validation issue for different java version(ie 1.6 and 1.8)
Scenario
1) xml document signed by using java 1.6
2) This packet is sent to the endpoint( this endpoint is hosted using Jboss Fuse (fuse-6.2.1.redhat-084) which uses java 1.8)
3)Due to Umarshalling(JAXB) Performed at this endpoint the signature packet structure gets Changed(Entire Signature Information gets appended to single line).
4)Validating this packet using signature.validate(valContext) [javax.xml.crypto.dsig.XMLSignature.validate] fails despite of the proper certificate available .
Is there a way with which Structure remains intact or signature.validate(valContext) returns true despite of structural change(As only structure changes not the content of the packet)