I just found that when I click on the search link on the home page the pop up box is hidden behind the advertising banner. Although it works from the thread entry page. Its the NOW 65 banner.
JK - FYI (in case these ads have disappeared by the time you investigate this) these are FLASH based adverts which appear in the banner at the top of the home page (and other pages with banner at top). They are obviously set up to be "at the front"/"on top" of everything (at least in IE6). When the dropdown search of quicklinks menu is selected the menu drops behind the advert.
I have put a block on that advertiser which should take effect in the next few hours. In the meantime I'll email Google to see what they have to say about it.