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The failure is occurring on the Jenkins master. The Jenkins master also needs access to the build toolkit when starting the build. If the Master is running on Windows, the /var/appl/... path is not going to be able to be treated as an absolute path.
I see from the trace:
Local Build toolkit="/var/appl/jenkins/rtctoolkit-4.0.1/jazz/buildsystem/buildtoolkit "
Node Build toolkit="/var/appl/jenkins/rtctoolkit-4.0.1/jazz/buildsystem/buildtoolkit"
I am wondering if you have setup toolkit directories appropriately. When configuring Team Concert (in the Jenkins configuration) you should be able to test the connection successfully. For the slaves you will need to configure where the toolkits are located. See https://wiki.jenkins-ci.org/display/JENKINS/Team+Concert+Plugin#TeamConcertPlugin-Master%2FSlaveConfiguration.