It is fine the way it is. In fact, if you have not noticed yet, your site is using the points the plugin states and the ones you expect (based on your question). If you see the users in your site they all have points finishing in zero.
There is a setting in admin/points which you can find at the Multiply all points. That is responsible of adding the extra zero. If you don't like having the extra zero, just switch it to 1. This will fire a point recalculation, BTW.
