Two Problems - old "settings" loaded and deleted services "returned"
1. It appears that the Dude reloads the "original" database when being rebooted, any changes or new additions are lost on reboot. Our work around is to "backup" the database, but this means we sometimes overlook a new client on reboot all info on that client is lost.
2. We only monitor certain services on our network, therefore we delete all other services including the dreaded 50:50, but on reboot all of the services are returned and if the dude is "rebooted" when we are asleep we will receive over a thousand email notifications by the time we wake up 6hours later.

Any suggestions or links to fixes would be appreciated.

Try last RC version, with 6.37 I had same issue.
I could not even reboot via winbox with this version.