Jenkins configuration is lost after  safeRestart or Restart, is happening in all our Jenkins instances

Configuration that is lost:

• Global security -> Matrix-based security : users and groups are missing, just 'original' configuration remains, I mean, all those users and groups generated at first time when Jenkins instance is provisioned.
• Master executor changed from 1 to 0

From script console: "ls -lrt /var/jenkins_home/".execute().text

Before restart:

drwxr-xr-x 4 root root 4096 Jul 9 12:20 backups
drwxr-xr-x 154 root root 28672 Jul 9 12:42 plugins
drwxr-xr-x 4 root root 4096 Jul 9 12:45 users
drwxr-xr-x 4 root root 4096 Jul 9 12:45 jobs
rw-rr- 1 root root 131 Jul 9 12:45 queue.xml.bak
rw-rr- 1 root root 16343 Jul 9 12:45 config.xml
rw-rr- 1 root root 7 Jul 9 12:45 jenkins.install.InstallUtil.lastExecVersion
rw-rr- 1 root root 0 Jul 9 13:03 ThinBackup Worker Thread.log

After restart:

drwxr-xr-x 4 root root 4096 Jul 9 12:20 backups
drwxr-xr-x 154 root root 28672 Jul 9 12:42 plugins
drwxr-xr-x 4 root root 4096 Jul 9 12:45 users
drwxr-xr-x 4 root root 4096 Jul 9 12:45 jobs
rw-rr- 1 root root 131 Jul 9 13:06 queue.xml.bak
rw-rr- 1 root root 156 Jul 9 13:06 hudson.model.UpdateCenter.xml
rw-rr- 1 root root 907 Jul 9 13:06 nodeMonitors.xml
rw-rr- 1 root root 121 Jul 9 13:06 de.theit.jenkins.crowd.CrowdSecurityRealm.xml
rw-rr- 1 root root 7 Jul 9 13:06 jenkins.install.InstallUtil.lastExecVersion
rw-rr- 1 root root 0 Jul 9 13:06 ThinBackup Worker Thread.log
rw-rr- 1 root root 262 Jul 9 13:06 jenkins.model.JenkinsLocationConfiguration.xml
rw-rr- 1 root root 271 Jul 9 13:06 hudson.tasks.Mailer.xml
rw-rr- 1 root root 1401 Jul 9 13:06 hudson.plugins.emailext.ExtendedEmailPublisher.xml
rw-rr- 1 root root 747 Jul 9 13:06 com.cloudbees.jenkins.plugins.bitbucket.endpoints.BitbucketEndpointConfiguration.xml
rw-rr- 1 root root 932 Jul 9 13:06 hudson.plugins.sonar.SonarGlobalConfiguration.xml
rw-rr- 1 root root 686 Jul 9 13:06 hudson.plugins.sonar.SonarRunnerInstallation.xml
rw-rr- 1 root root 228 Jul 9 13:06 javaposse.jobdsl.plugin.GlobalJobDslSecurityConfiguration.xml
rw-rr- 1 root root 16426 Jul 9 13:06 config.xml

Thanks in advance