Make sure you have DMA turned on for the disk. My mouse was extremely sluggish during heavy disk operations until I figured this out. Now it's smooth under both USB and PS/2 (I have two mice hooked up to my system).
My guess is USB is more work; the number of events coming into the processor should be the same, but there's more layers of software drivers and request routing to go through for USB.
es I agree with your answer there, because I felt also that USB has MoBo drivers, then OS drivers and then the actual driver for the mouse itself gets installed too, I knida see where you're getting at, but come to think of it maybe the speed of the USB bus compensates for that.
Beer is the devil's piss.
Something similar happened to me. It's because I have an ATA100 harddrive and Windows 2000 which automatically thinks the harddrive is ATA66. It'll get all laggy when the harddrive is active. I got that changed and now its working great.