ashtindell technically, settings cannot be deleted from the database unless they were either reset on the Settings Area or AAM plugin was reinstalled.
If none of the above happened, then I believe it is related to the fact that you've upgraded AAM to the latest 6.1.1 release from AAM 5 and some of the settings were not converted properly.
Please explain in more detail what exactly you are trying to define and I'll be able to help you to setup it properly. 9 out of 10 times, users overuse content access settings.
Keep me posted.