Is it smooth navigating the BIOS?
If not it's probably the motherboard or an attached device causing issues with the USB bus.
(I assume it's fairly new and not something obvious like the mouse pad)
If it IS smooth in BIOS then it's a software issue in Windows. That's harder to narrow down but see where you are first, then you can look at MSCONFIG to run simple bootup, experiment with disabling software on startup etc.