The mouse scrolling in GC has always been more of a "grab and pull" kind of thing (click and hold the left mouse button then pull the map in the direction you want to move it), instead of the edge scrolling many other games employ. Personally I have generally found (I most often use windowed mode) that edge scrolling is more difficult to use.
Another way to reposition the main map is to click on the mini-map where you want the main map centered.
