I have seen it do the periodic updates in double the specified time interval. eg when set to be every 6 hours it was actually doing it every 12 hours.
you can enable debug logging on the server and restart the server and look at the Plex Media Server.log files
Logs are recycled when they reach 5Mb in size or on restart.
Latest Log file is Plex Media Server.log, previous one is Plex Media Server.log.1 and prior to that Plex Media Server.log.2
Oldest log file Plex Media Server.log.5
Logs should have entries like this
DEBUG - Running scheduled update
INFO - It's been xxxxxx seconds, so we're starting scheduled library update for section xx (<library name>)