What's more likely is that the update changed your browser's Security or Privacy options to a higher level. Look under Explorer's TOOLS > INTERNET OPTIONS and poke around for places where either new windows or scripting may have been disabled.
Thanks vm for the welcome. Very interesting site that you have here, lots of good stuff.
In relation my problem I went thru everything, even tried setting to minimum security but got knowhere. Problem actually got worse in that child windows opened by normal href links were not spawning properly.....
In the end I reloaded IE6 with SP1 and the problem has now gone away.