I've just got a snapshot of the latest ispconfig3 and very nice it is, however I noticed something. Its using AJAX to login. Now I've been down this path recently on a project and I'm sorry to say it can cause problems, particularly with IE6. The problem seems to stem from the way the way the browser handles cookies (somehow the XML_HTTP_REQUEST cookies aren't registered properly) and after a couple of days messing about I reverted back to the "traditional" $_POST approach. Hope this nugget helps.
Thanks, but the login procedure is working fine for me in all current browsers. When you find a bug in the login procedure, I can check it out.