I don't see any errors. The clue here is that this was a gradual issue, where after applying changes, it took longer and longer to get services to start showing up to now where it never completes. So what is happening during that process?
messages.log
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Sep 15 12:27:11 kdcnagxi01 rsyslogd-2177: imuxsock begins to drop messages from pid 8112 due to rate-limiting
Sep 15 12:27:24 kdcnagxi01 rsyslogd-2177: imuxsock lost 3223 messages from pid 8112 due to rate-limiting
Sep 15 12:27:24 kdcnagxi01 nagios: Successfully launched command file worker with pid 8250
Sep 15 12:27:24 kdcnagxi01 nagios: Caught SIGSEGV, shutting down...
has a bunch of warnings about check intervals and notifications but i didn't want to include as it shows a lot of our server names etc.
mysqld.log
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150912 18:50:42 InnoDB: Completed initialization of buffer pool
150912 18:50:42 InnoDB: Started; log sequence number 0 44233
150912 18:50:42 [Note] Event Scheduler: Loaded 0 events
150912 18:50:42 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution
150915 12:11:44 [Note] /usr/libexec/mysqld: Normal shutdown
150915 12:11:44 [Note] Event Scheduler: Purging the queue. 0 events
150915 12:11:44 InnoDB: Starting shutdown...
150915 12:11:47 InnoDB: Shutdown completed; log sequence number 0 44233
150915 12:11:47 [Note] /usr/libexec/mysqld: Shutdown complete
150915 12:11:48 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150915 12:12:41 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
150915 12:12:42 InnoDB: Initializing buffer pool, size = 8.0M
150915 12:12:42 InnoDB: Completed initialization of buffer pool
150915 12:12:42 InnoDB: Started; log sequence number 0 44233
150915 12:12:42 [Note] Event Scheduler: Loaded 0 events
150915 12:12:42 [Note] /usr/libexec/mysqld: ready for connections.
Version: '5.1.73' socket: '/var/lib/mysql/mysql.sock' port: 3306 Source distribution
I'll PM you the check, it will have the similar output as messages but has the warnings that I was talking about.