On a (relatively big?) jenkins installation (~640 jobs and ~2200 folders and subfolders under jobs/ folder) it seems that scm-sync gets confused whether add or just commit config files and ends up in conflict situation. Besides of a size, this jenkins has almost zero idle time, meaning: there is allways some project running.

following logs are repeated:
—
tail /var/log/jenkins/jenkins.log
SEVERE: [checkinFiles] Problem during SCM commit : svn: E155004: Commit failed (details follow):
svn: E155004: There are unfinished work items in '/var/lib/jenkins/scm-sync-configuration/checkoutConfiguration'; run 'svn cleanup' first.
May 21, 2013 10:29:49 AM hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness processCommitsQueue
SEVERE: Error while processing commit queue : Error while checking in file to scm repository
[INFO] SVN commit directory: /var/lib/jenkins/scm-sync-configuration/checkoutConfiguration
May 21, 2013 10:29:49 AM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
SEVERE: [checkinFiles] Problem during SCM commit : svn: E155004: Commit failed (details follow):
svn: E155004: There are unfinished work items in '/var/lib/jenkins/scm-sync-configuration/checkoutConfiguration'; run 'svn cleanup' first.
May 21, 2013 10:29:49 AM hudson.plugins.scm_sync_configuration.ScmSyncConfigurationBusiness processCommitsQueue
SEVERE: Error while processing commit queue : Error while checking in file to scm repository
—

After day or two jenkins' java prosess takes all available CPU power and practically forces to reboot jenkins.

Feel free to ask more detailed logs if necessary.