With the 10.4.11 upgrade came Safari V3. It looks neat, but I started having issues with closing Windows. It turns out the SIMBL input manager that I was using on Safari was conflicting with it. By deleting ~/Library/InputManagers/SIMBL it fixed the issue.
On the same theme, here has been a lot of talk lately about Input Managers and whether they will be completely removed in Leopard. Just recently David Watanabe blogged about the uncertain future of Inquisitor.
It would be a shame for such an awesome Safari extension to become extinct, but thankfully Input Managers are not the only way to skin this cat.