hey , i think yo can't use both of features . you must disable "Remove write permissions from .htaccess and wp-config.php" in Better WP Security, if you want to use W3 total cache , coz "Remove write permissions from .htaccess and wp-config.php" make a file permission to 444 (Read, Read, Read). W3 total cache need permission to write file (wp-config and htacces), u can disable this setting or you can make your file permission to (644) via ftp .
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