I have installed Windows XP Service Pack 2.  The built in pop-up
blocker in IE blocks legit pop ups.  Even if I turn the pop up blocker off,
it continues to block certain popups, not all.  I've tried running a
repair by booting off a SP2 CD, but I continue to experience the
problem.

Two suggestions:
- Add the site that you want the pop-ups from to the allowed sites list.
   In Internet Explorer go to the tools menu -> Pop-up blocker ->
Pop-up Blocker settings -> then type the URL into text box and click
add.

-Given that IE has a past of being overly insecure, I would suggest
that you look towards another more secure, more stable, less
problematic browser such as Firefox , Mozilla, or Opera. Firefox by
default has built-in pop-up blocking and is generally faster than IE.
You may download it from http://www.mozilla.org

Hope this helps.

I have already added the site to my list.  I also use FireFox, but
some sites obviously don't work due to the "open" nature of FireFox.

I'm just going to format by drive and rebuild it.  I think there's
some kind of scumware that I haven't been able to remove.