The login in squirrelmail is handled by either courier or dovecot and not postfix. But I doubt that your problem has to do with a authentication problem of these services, most likely it is an apache or browser issue with session permissions.
Regarding your postfix problem: Yes, yast destroys the config on a reinstall of a application. You have to download the latest ispconfig, run the update.php script and select to reconfigure services to fix this.
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