Jenkins seems to be the target for nohup in a script started via ssh, how can I prevent that?
If I understood the question correctly, Jenkins is killing all processes at the end of the build and you would like some process to be left running after the build has finished.
You should read https://wiki.jenkins-ci.org/display/JENKINS/ProcessTreeKiller
Essentially, Jenkins searches for processes with some secret value in BUILD_ID environment variable. Just override it for the processes you want to be left alone.
In the new Pipeline jobs, setting BUILD_ID no longer prevents Jenkins from killing your processes once the job finishes. Instead, you need to set JENKINS_NODE_COOKIE:
sh 'JENKINS_NODE_COOKIE=dontKillMe nohup java NameOfClass &'See the wiki on ProcessTreeKiller and this comment in the Jenkins Jira for more information.