Sometimes a forwarder app is accidentally deployed to an indexer. It is normally limited by the throughput of network bandwidth.
[thruput]
maxKBps = 256
Please try to use the command ./splunk cmd btool limits list thruput to check if the maxKBps is set to 0. Otherwise indexing rate of an indexer will be limited and not fully utilized the IO rate of the disk system.
You may also refer the link below showing that index_thruput is controlled by thruput value.
http://wiki.splunk.com/Community:HowIndexingWorks
