add some basic debugging statements to find out what is going wrong.
<?
$javascript1 = mysql_query("SELECT `js1` FROM users WHERE `username` = '".$_SESSION['username']."'") or die (mysql_error());
echo mysql_num_rows($javascript1).'<br />';
if (mysql_num_rows($javascript1) == 0) {
mysql_query("UPDATE users SET `points`=`points`+88 WHERE `username` = '".$_SESSION['username']."'");
mysql_query("UPDATE users SET `js1`=1 WHERE `username` = '".$_SESSION['username']."'");
} else {
echo ("You already beat this challenge.");
}
?>
Btw, you don't need to quote column names in your queries.