Success! Thanks to everyone who helped resolve the problem.
I removed the jar files xmlparserv2.jar, saxpath.jar, xdb.jar and
commons-codec-1.3.jar from the application and then the WAR file deployed OK on Glassfish b53 and on b41.
I did confirm that deploying exactly the same WAR that failed with the later build still worked with b41 so it does appear that the behavior change in how the JAXP parser is picked up since b43 was the cause.
John.
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