If you have it set up on localhost and configured the settings accordingly, it will remain on your localhost. Meaning that if you create a torrent with the announce url
http://localhost/announce.php, it will always connect to the localhost from the computer it's being run on.
So probably in the case of your box (assuming it's your box because of torrentflux), it is trying to connect to a tracker supposedly present on the box itself (=localhost).
Basically localhost is only usable for testing purposes, unless you've configured your pc to be used as server, which I doubt in this case :). If it's set up correctly, you can use your IP adress suffixed with the /announce.php as your announce url and start it on your box.
Regarding the CHMOD's; all files listed need to be CHMOD'ed, not just the one folder/file. It should give you a list of which files still need to be altered and which have been CHMOD'ed correctly.