I have a similar problem, also after the update. there is only the “cgi-bin” folder showing up under the “Excluded files and directories”. There is also a”fatal error” message. “Fatal error: Uncaught exception ‘UnexpectedValueException’ with message ‘RecursiveDirectoryIterator::__construct(/www/htdocs/*******/logs/) [recursivedirectoryiterator.–construct]: failed to open dir: Permission denied’ in /www/…” and so forth.
Since I don′t want any folders to be excluded anyway, I don′t need that option at the moment. Just want to make sure this error doesn′t affect anything important.