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I had the exact same problem. It turned out that restarting it with http://localhost:8080/restart didn't restart the daemon that reads the /etc/default/jenkins file. Doing sudo /etc/init.d/jenkins restart made it work.
After http://localhost:8080/restart it does not use prefix because only java has been restarted, not daemon:
> ps aux |grep jenkins
jenkins 5727 0.0 0.0 11996 364 ? Ss Feb21 0:00 /usr/bin/daemon --name=jenkins --inherit --env=JENKINS_HOME=/var/lib/jenkins --output=/var/log/jenkins/jenkins.log --pidfile=/var/run/jenkins/jenkins.pid – /usr/bin/java -jar /usr/share/jenkins/jenkins.war --webroot=/var/cache/jenkins/war --httpPort=8080 --ajp13Port=-1
jenkins 5728 241 7.2 1549816 280136 ? Sl 07:22 3:17 /usr/bin/java -jar /usr/share/jenkins/jenkins.war --webroot=/var/cache/jenkins/war --httpPort=8080 --ajp13Port=-1
Then restart this way:
> sudo /etc/init.d/jenkins restart
It now works because the deamon has been restarted:
> ps aux | grep jenkins
jenkins 5290 0.0 0.0 11996 364 ? Ss 07:25 0:00 /usr/bin/daemon --name=jenkins --inherit --env=JENKINS_HOME=/var/lib/jenkins --output=/var/log/jenkins/jenkins.log --pidfile=/var/run/jenkins/jenkins.pid – /usr/bin/java -jar /usr/share/jenkins/jenkins.war --webroot=/var/cache/jenkins/war --prefix=/jenkins --httpPort=8080 --ajp13Port=-1
jenkins 5291 152 3.7 1446928 144288 ? Sl 07:25 0:04 /usr/bin/java -jar /usr/share/jenkins/jenkins.war --webroot=/var/cache/jenkins/war --prefix=/jenkins --httpPort=8080 --ajp13Port=-1
I suggest this issue is resolved and closed.