*Update*
To save hassle, try running Darwinia in compatibility mode for Windows XP (Service Pack 2) before trying the method below. I stupidly forgot to try this first and this method was also successful in fixing the mouse problem.
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The problem: It is well known that in the latest version of Darwinia the mouse will move very slowly and stutter in-game when in full screen mode.
The simplest, most common workaround is to play in windowed mode. This works for me, but I wanted to play in full screen without this slow mouse problem...
Others have reported that forcing VSync on in their video card control panels resolved the issue for them. However, this did not work for me.

But this did....

I saw someone on this page http://forums.introversion.co.uk/viewtopic.php?f=32&t=16484&start=30 post the fix that worked for them. They mention it being on a sticky somewhere so thanks to whoever!

**The solution**
Set the CPU affinity to one core! Simple as that.

To set core affinity, simply Alt-Tab out of the game, go to Task Manager, locate Darwinia (32 bit), right-click, then left click to select "Go to details", locate darwinia .exe (it should already be highlighted), right-click, now left-click "Set affinity, uncheck all-but-one of the CPUs, left-click 'OK' and return to the game.
Note: You will have to do this once every time you start the game - I think it's a small price to pay if it actually works for you as it did for me.