I was able to resolve this same issue by following the docs. In this particular app I was pushing the SSL config settings in the inputs.conf and the docs advises against that and states you will see this error because of this. I had to manually add the lines in that file to each indexer and remove the inputs.conf from the app and that fixed my issue. Hopefully this helps you as well.
http://docs.splunk.com/Documentation/Splunk/6.2.5/Indexer/Updatepeerconfigurations
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