Does this happen regardless of what you search for? I often find that if I search for some complicated regexp, it might take much longer, and for a while I'd be seeing the beachball. It often takes a while until I regain control, so long in fact that I've considered killing it many times. Are we talking here about files with very long lines, or just with too many lines? Are they local or remote?
Can be any simple search string
The files are either a 20-100mb mysql dump, which likely means very long lines, or a hundred word doc files. neither is even relevant to the project, but because i just open the projects with "e .", they end up in it. (where e is an alias for mate or open -a textmate)
They're local
If I wait a few aeons, sometimes I can regain control, but sometimes it goes so resource hungry I just kill it.