I started having this problem (I think) when I updated to 10.4.9. My issue is that the "main spotlight" interface doesn't work - that is, when I press cmd-space and type in a search I get nothing - not even a "no results" message. Spotlight works, however, if I access it from a finder window. So, the index is there and the search IS working, but not from all the search locations. I've tried rebuilding permissions, but to no avail. Any tips? Thanks!