Hiccups

This has shown up on several upgrades of Win98SE to Win2k: this pc is AMD K6 1.3MHz, 512 MB RAM, 20GB HDD. After upgrade, it seems like o/s has to “stop, and think about” the last request made of it: move the mouse, and two to 5 seconds later thecursor goes where it should be. All input seems to hesitate. This is a dual-boot system – Win98SE does not show these symptoms. Any ideas?