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Running the .conf file is probably not what you want to do, since it's just the configuration for logrotate (thinking it was a typo, but making sure ). I don't think the default install usually has a 'mysql' anything in logrotate.conf, but many popular distros have a /etc/logrotate.d/ directory as well, that contains package specific log rotation needs. A 'mysql' logrotate config file might be in there, and might be problematic. Just to get it going, you might open up that file and comment out each configuration line (just put a # in front of it), and see if that works. If it does, then it will be easier to narrow down the exact problem.
Am I to assume that syslogd also executes /etc/logrotate.conf? If so where is this documented? So far I've read what gets done but not how it gets done.
I don't think execute is the proper term here...but I think we're on the same page anyway. *.conf files are usually "read in" by their respective programs, and are I guess executed within the program, but it isn't a true execution. They generally direct their owner on how to execute.
As far as the automatic execution goes... You might want to check the /etc/cron.* directories (if you have them) for something related to logrotate. There are usually /etc/cron.d, /etc/cron.hourly, /etc/cron.daily, /etc/cron.weekly, and /etc/cron.monthly. As you might guess, hourly goes off every hour, daily every day, etc, so long as it's setup in the crontab (usually is by default). Anyway, I'd be willing to bet that within one of those (probably daily), you'll find something related to logrotate.