Do you have any "enhancers" that constantly "spam" system with windows messages? This could be just anything - antivirus, additional desktop candy, etc?
The idea is that DOS extracts windows messages in a loop one by one and processes them. On Windows it extracts only one message per frame. This means that if application queue is filled with some 'trash' messages you will definitely have severe input lag.
If you're a developer - I'd suggest checking this stuff using WinSpy++ stuff, in other case just try to make your system as free from any add-ons as possible. Close browsers, terminate downloaders.. Then try and see whether it makes any difference.
