We have two configurations, each with an instance. The first config/instance has been running just fine since Nov 2010. The second configuration is found to be not running every couple of weeks or so. I haven't seen anything in the logs (wow, which ones??) that indicate a failure causing the instance to stop.
I can't see or haven't noticed that the entire server is restarting and then leaving this instance not running, so I really don't know where to start troubleshooting.
From the admin GUI, I don't see a setting for either the configuration or the instance that says to startup automatically or not.