A while ago I wrote an article on how to get your hands on a copy of IE 5.5 Beta. For more information on that, check out http://www.serverwatch.com/tutorials/article.php/2179371
Well, if you did decide to load that demo copy of IE onto your machine and you attempted to upgrade that specific machine, regardless of it's level of Windows OS, you will notice that once you have W2K, you no longer have IE 5.5.
What has happened is that the upgrade has actually downgraded your browser to the version that is included with the OS.
One must keep in mind that this is a Beta version of IE and that they did not take it into account when creating the upgrade for W2K (although they probably should have). You can be sure that this will be remedied at some point prior to or close to the official release of IE 5.5.
To resolve this issue, simply reload IE 5.5 on your upgraded machine. I know this is not the resolution that you are looking for, but it is the best that I can do.