I am not sure if this is the same thing but I have noticed, especially with video, avis, divx etc, that when you click on the file concerned (and it opens up the in the next column/whatever with a big icon and some file details) if the files are incomplete or corrupt the machine WILL die in the bum while it tries to either render a small preview movie or make sense of the audio track in question.
I find it very helpful having menu meters installed as major slow downs usually involve the CPU being maxed out. Without something to tell you it IS maxed you have to use guess work which is fine if you have a good idea that this may be the case but no good at all if you don't.
PS sorry if this does not make complete sense. If you have no idea what I am talking about i'll try again and include a screen shot to illustrate the points I have made.
cheers, kim