Sorry, We're having trouble explaining ourselves.
I understand that the config file shouldn't be regenerated randomly, but my settings are reverting back to default without me doing anything. The server is not rebooting, i'm not running any post-upgrade... server runs fine then 'randomly', i get problems, check those settings and they've reverted.
I'm not editing any files at all, I don't edit config files. I log into the server (ssh), type 'mysql' to log into the mysql command line interface, then issue the commands in my first post.
Doing this makes everything work. This worked flawlessly with no issue for over a year. No reboots, no issues.
Recently, every now and then ('randomly') these settings revert back with no interaction from me. To fix, I reboot server and reissue the commands.
I hope I've explained properly
Thanks
EDIT:
janet - the commands are in my first post. 4 commands are issued, all timeout related. I'm not sure I need all 4 but doing that makes everything work and i've not had problem before. thanks