Hi MarcvR,
I have a few questions about this CAT:
1) What 'brand' of CAT was it?
2) Did you take the Essay and IR sections before starting the Quant section?
3) Is this the first time that you've encountered this 'error' (your computer shutting down and the timer being 'off?'
The scoring algorithm on the Official GMAT is far more complicated than most people realize. It takes into account a number of different factors, including the relative difficulty of the question, whether you were expected to get it correct or not, the placement of the question, what's going on "around it", the "strings" of correct and incorrect answers, whether the question even counts or not (some questions are "experimental" and are worth 0), if you leave questions unanswered and incur a penalty, etc. As such, you shouldn't be spending time trying to figure it all out. You'd be better served working on building up your skills.
As far as keeping this problem from happening again, you should be able to change the Power Settings on your computer so that it does not shut down so quickly when not actively being used.
GMAT assassins aren't born, they're made,
Rich