This happened on a new server installation an a fully loaded Mac-mini running Lion 10.7.2. This is a new machine and a new server package from FileMaker. For at least the first several times we restarted the machine, it would come back up with the button UNCHECKED! It eventually stuck and we are monitoring this check box.
BEWARE! Since we often don't restart our servers for extended periods, it might be a good idea to monitor this check box. You could end up without a backup.
I spoke with FileMaker support as well. They indicated that they had a report that server would "reset" itself upon restart - they did not receive any secific information. This is the only change we saw.