Ok now do these steps and let me know if the root htaccess file (auto_.htaccess) is quarantined again.
1. Go to the B-Core > htaccess File Editor tab page > click the Lock htaccess File button > click the Turn On AutoLock button.
2. Go to the Security Modes tab page > click the Create secure.htaccess File button > select the Activate Root Folder BulletProof Mode Radio button and click the Activate|Deactivate button.