I reached out to the Cassandra mailing list. This is the issue: https://issues.apache.org/jira/browse/CASSANDRA-6298
This is OEL6, Java 6. It happens with the nodetool or CLI. It may be due to multiple data directories existing. See the bug for more details.
CASSANDRA-6298 was reported against 2.0 beta 1 and the patch looks like it is specific to leveled compaction. RHQ uses size-tiered compaction. I am not sure if this is actually related to the issues you are seeing. Are you using multiple data directories?
C-6298 is the issue I filed, and yes I am using multiple data directories. I referenced the wrong bug in my bug. The related one is CASSANDRA-6093.