Check the htaccess file in Quarantine using the View File option to see what has been added to the Root htaccess file that caused it to be quarantined. Typically what causes this issue is that a plugin will write the default WordPress Rewrite htaccess code at the bottom of the Root htaccess file, which should not be done, but it is a very common problem. If you are not sure what has been added to the Root htaccess file then copy the Root htaccess file contents in your forum reply. So I can take a look at it.
You can lock your Root htaccess file to prevent other plugins from writing to it. Go to the BPS Pro > B-Core > htaccess File Editor tab page > click the Lock htaccess File and Turn On AutoLock buttons.