I also encountered issues with 2.1 with characters being scrubbed out of remote commands, both via individual server remote commands and SSM remote commands. Have you looked at this thread?
https://www.redhat.com/archives/spacewalk-list/2014-May/msg00086.html This should help your issues - after both fixes were applied, we are no longer having issues with >> being scrubbed from jobs. Best of luck!
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