Although it was interesting to see how many things it repaired, since I just did it like 72 hours ago, before I upgraded, the permissions repair (in safe boot) also did not remedy my disappearing search results window.
I don't know if it has any sort of significance, but the machine I'm running is a b+w g3 with a g4 upgrade. That right there has seemed to cause a few little problems for me with certain software. I didn't think with the way Limewire is programmed and run that that would make any sort of difference, but you never know. Maybe somebody else is having the same problem. I saw some other guy's posting with the same problem, but he just upgraded to 10.4 and fixed it. I can't upgrade to 10.4, maybe I can to 10.3, but I probably won't be able to do that for awhile.
If anybody has a fix for that in the meantime, that would be AWESOME. Otherwise, it'll just be a kick in the butt for me to upgrade my system software.

BTW: MERRY CHRISTMAS/HAPPY HOLIDAYS to anybody reading this, and especially responding. It's a weird time to be up and talking about computer crap online when you should be getting up at like 7am to call your family and wish them a Merry Christmas.