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Some more info:
This seems to be happening on Maven job type builds when the build state goes from Green (all unit tests pass) to Yellow (1 or more unit tests fail). As long as tests are passing we have not seen this issue. As soon as test fail or start to "flap", the job gets into this weird state where builds fail with the NPE.
We're considering moving away from the Maven job type after reading: http://javaadventure.blogspot.ie/2013/11/jenkins-maven-job-type-considered-evil.html