Cpanel shutting down ALL MySQL instances on server

[Mr. Bob]

I have two separate MySQL installs and whenever Cpanel updates MySQL, as it did last night, it will shut down all instances of MySQL on the server. This is a problem for me as the other MySQL instance is not in any way tied to Cpanel. For now, I've setup a cron to make sure the other instance is running and if not then auto start it. But obviously I'd like to avoid this issue altogether. Any way I can stop Cpanel from shutting down all instances?

Running CentOS 5.3 here.

Restarting MySQL "normally" through init.d does not do this, so I'm certain whatever Cpanel does during the restart process is causing it.