More detailed log:

Aug 16, 2013 8:50:22 PM hudson.plugins.scm_sync_configuration.SCMManipulator addFile
FINE: Adding SCM file [jobs/emahdil_env/config.xml] ...

Aug 16, 2013 8:49:27 PM hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy
SEVERE: [deleteHierarchy] Problem during remove : The git command failed.

Aug 16, 2013 8:49:27 PM hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy
FINE: Deleting SCM hierarchy [/proj/eis_jenkins/prod/managed/jenkins_home/scm-sync-configuration/checkoutConfiguration/jobs/emahdil_env] from SCM ...

Aug 16, 2013 8:49:27 PM hudson.plugins.scm_sync_configuration.SCMManipulator addFile
SEVERE: Error while adding SCM file : /bin/sh: git: command not found

Aug 16, 2013 8:49:27 PM hudson.plugins.scm_sync_configuration.SCMManipulator addFile
FINE: Error while adding SCM file : /bin/sh: git: command not found

Is there a temporary fix for this? to get config's backed up again?

Seems like the git command is not found on your master.

Do you already succeded to commit/push files before ?

Sorry for delayed response!

Yes. we succeed in add, commit and push. What we have noticed is, this occurs on Deletion of job. We tried deleting a job and here is the detailesd log:

SCM Sync status :
Wed Aug 28 15:48:26 EDT 2013 : Delete jobs/Simple-job
Wed Aug 28 15:59:23 EDT 2013 : Delete jobs/Simple-job

To remove this message, please remove JENKINS_HOME/scm-sync-configuration.*.log files

Aug 28, 2013 3:48:26 PM hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy
SEVERE: [deleteHierarchy] Problem during remove : The git command failed.
Aug 28, 2013 3:48:26 PM hudson.plugins.scm_sync_configuration.SCMManipulator deleteHierarchy
FINE: Deleting SCM hierarchy [/proj/jenkins/prod/emc/jenkins_home/scm-sync-configuration/checkoutConfiguration/jobs/Simple-job] from SCM ...
Aug 28, 2013 3:48:26 PM hudson.plugins.scm_sync_configuration.SCMManipulator addFile
FINE: Added SCM files : [jobs/Simple-job/config.xml] !
Aug 28, 2013 3:48:23 PM hudson.plugins.scm_sync_configuration.SCMManipulator addFile
FINE: Adding SCM file [jobs/Simple-job/config.xml] .../log/scm_sync_configuration/
Aug 28, 2013 3:48:11 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checked in SCM files !
Aug 28, 2013 3:48:04 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checking in SCM files ...
Aug 28, 2013 3:45:57 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checked in SCM files !
Aug 28, 2013 3:45:54 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checking in SCM files ...
Aug 28, 2013 3:37:24 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
.
.
.

> more $JENKINS_HOME/scm-sync-configuration.fail.log

Wed Aug 28 15:48:26 EDT 2013 : Delete jobs/Simple-job<br/>Wed Aug 28 15:59:23 EDT 2013 : Delete jobs/Simple-job<br/>Wed Aug 28 16:05:27 EDT 2013 : Delete jobs/2DEL-precom_13b_cp1_
maint<br/>Wed Aug 28 16:07:13 EDT 2013 : Delete jobs/Simple-job<br/>Wed Aug 28 16:07:16 EDT 2013 : Delete jobs/Simple-job<br/>

> cd $JENKINS_HOME/scm-sync-configuration/checkoutConfiguration

> git status

1. On branch master
2. Changes to be committed:
3. (use "git reset HEAD <file>..." to unstage)
   #
4. new file: jobs/2DEL-precom_13b_cp1_maint/config.xml
   #
5. Changes not staged for commit:
6. (use "git add <file>..." to update what will be committed)
7. (use "git checkout – <file>..." to discard changes in working directory)
   #
8. modified: config.xml

git status

On branch master
Changes to be committed:
(use "git reset HEAD <file>..." to unstage)
#
new file: jobs/2DEL-precom_13b_cp1_maint/config.xml
#
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git checkout – <file>..." to discard changes in working directory)
#
modified: config.xml

Seems like changes gets hung in Git index. It doesn't get committed. I manually committed it and delete the log 'scm-sync-configuration.fail.log' and everything is working as before.

Aug 28, 2013 10:27:30 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checked in SCM files !

Aug 28, 2013 10:27:26 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checking in SCM files ...

Aug 28, 2013 10:26:29 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checked in SCM files !

Aug 28, 2013 10:26:28 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checking in SCM files ...

Aug 28, 2013 10:26:28 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checked in SCM files !

Aug 28, 2013 10:26:26 PM hudson.plugins.scm_sync_configuration.SCMManipulator checkinFiles
FINE: Checking in SCM files ...

The issue is easily re- generatable. by renaming or deleting the job.

Yep, a lot of issues are already filed.
Will mark these as a dupe of JENKINS-15128

Once it fails on job rename or delete, nothing can be done to make it work again...

Yep, you're welcome to provide a fix, project is open source "..."

what does below git command says?

cd <JENKINS_HOME>/scm-sync-configuration/checkoutConfiguration
git status

In our case, the changes were in Git index; I did a manual commit and removed the JENKINS_HOME/scm-sync-configuration.*.log file. It re-started to work.

I am getting the same error when trying to use the same git repository for 2 different projects.
It fails to sync the main config.xml including the plugin config files:

"SEVERE: Error while adding SCM file : /bin/sh"

FYI, JENKINS-15128 was fixed in 0.0.8