Remember that config files are regenerated from templates. So unless you have a hacky template, or template override, a signal-event post-upgrade/reboot should sort out your configs.
One thing to check.... what is the server load like? Just wondering if you have had a hack of some description that is putting a high load on the server?? Just a thought.
If we suspect it might be a config issue the two things to look at are what other contribs have you installed that may affect things, and what do your logs say?
You can generate a report of new rpms etc from server-manager (can't remember where exactly)
Or use newrpms from this:
https://wiki.contribs.org/Audit_ToolsIf you have a lot of info I'd suggest posting on say pastebin after removing anything sensitive.
Troubleshooting email here
https://wiki.contribs.org/EmailCheck your messages/qpsmtpd/qmail/sqpsmtpd logs for errors:
https://wiki.contribs.org/Log_FilesDon't just post swathes of stuff. Grep for errors and see what you can find.
https://wiki.contribs.org/Useful_CommandsSomewhere on the wiki are some grep commands that will look for errors or warnings in logs. Can't find it on mobile, and I'm about to take off.... !