JankyLV on "wp-config keeps adding new lines"

My page had some malware on it, so I deleted all the files from root directory, wp-admin and wp-includes. Copied from fresh install. After an hour or two there was white screen of death. Couldn't figure out what was wrong until I realised that wp-config.php was changed.
Only changes made to it were one line at the bottom just before the last line:
require( ABSPATH . 'wp-admin/setup-config.php');
How can I stop this from happening?