A good place to start would be to graph what is going on use the built in performance monitor. CPU and disk usage would be a good place to start. You can end up with very low CPU but something is smashing the disk and everything seems jittery. This was how I figured out why vista ran like crap (prefetcher and indexer). In win7 they fixed it.
You can set performance monitor to monitor over long periods and then open the file back up and look at the whole time to see what is going on. I used to use it to help find if an application had a slow motion memory leak. But it should show you if something odd is going on. If you are using vista and up resource monitor is a good thing to take a look at as well.
Previous 
Index 
Next 
Flat 
Re: Strange observation...
Reply
