Recommendation: Run the "splunk diag" utility, open a case and upload the diag file to your case, Splunk Support will provide you assistance.
Here are a few things to check, according to the url listed below:
Check disk space on all of your partitions. If your space is too low, then that will cause indexing and searching problems.
Verify that "splunk-optimize" has been running. If you see a large number of *.tsidx files in your buckets, you can simply run splunk-optimize /path/to/your/bucket to force this process to run.
Try disabling some non-essential scheduled saved searches and see if that helps relieve the problem. (You probably don't want to do this for summary-indexing saved searches, if it can be avoided.)
http://splunk-base.splunk.com/answers/7996/down-error-skipped-indexing-of-internal-audit-event-will-keep-dropping-events-until-indexer-congestion-is-remedied-check-disk-space-and-other-issues-that-may-cause-indexer-to-block
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