So I found the cause of my problem, as it was also causing issues with other things on my system. It was 1UP Industries' Bins application. After uninstalling it, everything works perfectly fine! Apologies for the inconvenience.
I've currently got a 560ti. As an example, my CPU usage is currently at around 9/10%. When I launch a modern app it rockets up to around 25%, but after several seconds it settles back down again. Still a stuttering mouse whenever over the window when it's selected. The app itself isn't affected/doesn't slow down etc. Animations display correctly and smoothly.
Yea, it happens with each one, but only when they're the highlighted window. When they're not, the mouse doesn't stutter when over the top.
I have a Microsoft Comfort Mouse 6000. I only use the Microsoft Mouse and Keyboard Center, and neither in there or the Windows mouse settings is there an option for a high update mode, so I'm going to go with a no.
So I've just updated to Windows 8.1, updated ModernMix and Start8, and for whatever reason, when I have a modern UI application in windowed mode, whenever the mouse is over it, it stutters like hell. In fullscreen mode it's fine. Anybody else having this issue?