Sounds like you have two require once lines attaching the WA_SecurityAssist\Helper_PHP file to the page.
Double check the checkout page for more than one line that looks like:
<?php require_once( "WA_SecurityAssist/Helper_PHP.php" ); ?>
the path on the second one will be slightly differant, maybe:
<?php require_once( "User_Registration/WA_SecurityAssist/Helper_PHP.php" ); ?>
The second one can be deleted.