It may have been Skype. I recall that on a couple of occasions when I started Skype or when I had it set to start on boot it took ages to settle down.
I get the same effect when I start Limewire (file sharing prog). It does A LOT of processor intensive network activity, maybe a solid 3 minutes or so, before it frees everything up and the system returns to normal.
Try starting and stopping Skype a few times and see if there's a pattern.
Cheers
AA