I have a thread open regarding a problem with TimeMachine not docking however this is different. If you have, say a folder on your desktop that's been there at least a day or so look it up in Spotlight and see if Spotlight reads it on your external hard drive. Mine doesn't ever since I downloaded Leopard. Before if I had the folder on my hard drive, my external drive Spotlight would identify it in both places now however it will only identify anything(that has gone on to my external hard drive since installing Leopard) on my hard drive.