I have been able to consistently reproduce the thread death with "Stash Webhook to Jenkins" (v2.6) triggering a Multi-Configuration job. Our installation is relatively new, and this is the first time we setup anything to do triggering of jobs.

Log of session

Mar 27, 2015 2:39:52 PM INFO hudson.plugins.git.GitStatus$JenkinsAbstractProjectListener onNotifyCommit
Scheduling BUILD: Code Deploy to build commit 7410c63de6e0431ee7c831bfdc1f2ba909b00385
Mar 27, 2015 2:39:52 PM INFO hudson.plugins.git.GitStatus$JenkinsAbstractProjectListener onNotifyCommit
Scheduling BUILD: Code Deploy ยป py27 to build commit 7410c63de6e0431ee7c831bfdc1f2ba909b00385
Mar 27, 2015 2:39:52 PM INFO hudson.plugins.git.GitStatus$JenkinsAbstractProjectListener onNotifyCommit
PostCommitHooks are disabled on DEPLOY: code_deploy
Mar 27, 2015 2:39:52 PM SEVERE hudson.model.Executor run
Unexpected executor death
java.lang.IllegalStateException: /var/lib/jenkins/jobs/build_code_deploy/configurations/axis-TOXENV/py27/builds/8 already existed; will not overwite with build_code_deploy/TOXENV=py27 #8
	at hudson.model.RunMap.put(RunMap.java:187)
	at hudson.matrix.MatrixConfiguration.newBuild(MatrixConfiguration.java:284)
	at hudson.matrix.MatrixConfiguration.newBuild(MatrixConfiguration.java:74)
	at hudson.model.AbstractProject.createExecutable(AbstractProject.java:1205)
	at hudson.model.AbstractProject.createExecutable(AbstractProject.java:144)
	at hudson.model.Executor.run(Executor.java:213)

Mar 27, 2015 2:40:20 PM INFO hudson.model.Run execute
build_code_deploy/TOXENV=py27 #9 main build action completed: SUCCESS
Mar 27, 2015 2:40:21 PM INFO hudson.model.Run execute
build_code_deploy #9 main build action completed: SUCCESS
Mar 27, 2015 2:40:44 PM INFO hudson.model.Run execute
deploy_code_deploy #11 main build action completed: SUCCESS

Of interest Build #8 is the previous successful run, build #9 is the current run and succeeds in a different thread.

Versions

component version
Jenkins 1.606
Stash 3.1.0
Stash Webhook to Jenkins 2.60
ShiningPanda plugin 0.21

Job Configuration
Job Name: build_code_deploy
SCM: git (ssh)
Branches: */master
Poll SCM: H 0 1 1 *
Configuration Matrix: Tox; py27
Build: Tox Builder, $configuration_file=tox.ini, recreate (checked)
Post-build: trigger job= deploy_code_deploy, Publish JUnit test result, Notify Stash Instance

Stash Plugin:
Configured to only build from Master

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