I run Windows Update and I get the same 5 updates every time (Windows Vista Security Updates and Internet Explorer 9). I also install Internet Explorer 9 and it gives me the welcome to IE9 window when it opens, but then the update alway reappears.
I ran all 4 steps of the software (I read several other posts in the Forum about people having luck with the tool). After running all of the steps and restarting the computer, Windows Update came back with all 6 updates (all of the previous plus .net 3.5 update).