Do you have mapped drive connections that aren't always available? It could be something like that where its trying to do something that has to timeout before it proceeds. Download and fire up sysinternals process monitor - its free: http://technet.microsoft.com/en-us/sysinternals/bb896645.aspx It shows you all file activity so you can see what exactly is happening during those seconds of delay. Even on a machine that isn't have a problem its a great program to run to see what is going on in the background.
Thanks guys for all your suggestions. Well, defragging seems to have done the trick. I just started my after hours chart-saving routine for today, and so far so good.