This splunk blog post indicated that I could use S3 as the default FS, but switching to HDFS did solve the problem.
http://blogs.splunk.com/2013/11/13/analyze-data-with-hunk-on-amazon-emr/
For anybody that comes looking, I also had to add the following to my provider configs to get splunk to use the Hadoop 2 compatible splunkMR jars:
vix.command.arg.3 = $SPLUNK_HOME/bin/jars/SplunkMR-hy2.jar
vix.splunk.impersonation = 0
... View more