I have experienced the issue that logstash (when started as a service) does not read log files unless they are world readable or owned by the logstash user itself. I have added the logstash user to the user group of the files (in my case apache user group) and that did not work. Then I found a solution to the problem here:
http://serverfault.com/questions/632079/logstash-not-reading-logs-unless-world-readable