Check your user table and make sure the salt field is char(30), not char(3). Also, according to the announcement:
Quote:
Note: If a user changes their password after the patch is uploaded, but before the upgrade_402_salt.php, then they will be unable to log in. The password will need to be reset after the upgrade_402_salt.php. Setting the site to be offline while the patch is applied will prevent users from changing their passwords during this interval.
So, if you forgot to run the script, all the new users since you uploaded the files, or users that tried to set their passwords since then, WILL have problems.