Additional settings are automatically deleted

Did you notice this after certain changes/updates?
Are there specific or random additional settings involved?

I would check to see if you have that same setting disabled at another level. to verify where the settings are applied you can use this report. make sure there are not two or more client groups where one group has it enabled and the other has it disabled.

report - https://cloud.commvault.com/webconsole/softwarestore/#!/135/663/11243

Are you adding these settings in the Additional Settings section in the CommCell console or are you manually adding them to the registry?

version is V11 SP13 

SP13 is almost 4 years behind the current maintenance release.  Do you have plans to upgrade anytime soon?  Also can you please answer the following question:

Are you adding these settings in the Additional Settings section in the CommCell console or are you manually adding them to the registry?