Apparently the fix for MS03-032 changed the way IE interprets relative URLs when opened by javascript, resulting in “Page not found” errors. According to MSKB 827667 (or this download from the Microsoft Download Center), the new update will address this issue.
How? I dunno, the article is less than clear to me. I s’pose it changes the assumed base of relative URLs back to what it was BEFORE MS03-032. If you’re getting errors when you try to open a web page by clicking on a button in a web page (remember, this is a javascript issue, not a link issue, per se) then apply this patch.