I started having mouse problems after upgrading to Windows 8.1 when playing Ace of Spades. I was almost convinced that it was a hardware problem.
Turns out that Microsoft changed the mouse polling for 8.1. Microsoft has a patch for this at KB2908279. I downloaded and ran the "Microsoft Fix it" on Ace of Spaces. After running, I had to reboot. After rebooting I ran the game with no change...still lots of mouse stutter.
The KB2908279 fix it recommended checking KB2907018 and KB2907016. KB2907016 is the "Disable display scaling on high DPI settings" and it did the trick for my hardware/software setup.