Thanks for sharing your setup details.
I worked around the problem by not using Logstash in my implementation. I used nfcapd and nfdump for capturing the logs and indexing the fields of interest into ElasticSearch. So my setup looks like:
"nfcapd background service" => cron job("parse using nfdump" => "index into elastic search") => kibana
Since couple of folks apart from me have reported this issue, I have filed a bug in github for this issue - https://github.com/elastic/logstash/issues/4165