If you couldn't change the plugin, maybe you can't delete it either. You'd have to check in the modx_site_plugins table in the database to see if you really deleted it (I'm guessing not). So it's appearing to come back because it was never really gone.
I can't think of a System Setting that would do this. Are you sure you weren't messing with the permissions on a Policy, or changing the Policy in an ACL entry? That would explain what's happening.
To see if it's permission-related, try this:
- Update your user profile and make yourself a sudo user.
- Flush permissions and flush all sessions.
- Delete all files in the core/cache directory
- Log back in.
If your problem is gone, it was a permission/policy issue.