An Update:
I recently purchased Tomb Raider: Legend and encountered the same problem as I had with Penumbre: Overture, that is the mouse lags but everything else runs smoothly. So I though dammit I'm going to get to the bottom of this. I suspected it must be some process running in the background so using the list here:
http://www.sysinfo.org/startuplist.php
I went through and disabled all the unneccessary startup processes in MSCONFIG. And what do you know it worked! I didn't make note, or go through it in a methodical enough fashion to work out just what process was causing the problem but I would suspect one of the mouse/keyboard processes for fancy functionality.
Anyway hope this maybe helps someones else.