Why Is Clicking The Minimap Imprecise When I Am Zoomed In?
This applies to the Pre 4.0 version only. In the current Unity 4.0 version the minimap has been reworked from the ground up and now is a full screen overlay. Use the "T" key in the planet view or the "MAP" button lower left anytime to open the new minimap. The rectangular box represents the visible field of the planet map, and will change as you zoom in and out. The outer ring indicates the boundry of the slow speed zones. Ship speed is limited to 16 or less at the outer ring, dropping to a max speed of 8 a little further out (even farther out is the max speed of 2). The inner ring represents the limit of the buildable area.
Pre 4.0 A: The individual planetary battlefields in AI War are immense -- the simulate thousands of square kilometers of area. The minimap, by necessity, is quite small in comparison. This makes it so that a single pixel on the minimap correlates to around two square km of area. So when you click a specific pixel, it centers you in that 2km^2 area, but that might not be right on top of the ships you are wanting to see if you are zoomed all the way in.
This problem is not one unique to AI War -- in Supreme Commander, for instance, the problem was so severe with their larger maps that their game does not even show the minimap by default. In our particular game we felt like the minimap was helpful and important (and we felt blind without it, as longtime RTS players ourselves), but clicking the minimap is best done when you are at least partially zoomed out. As you play, you'll get a feel for what works best and what you are most comfortable with.
In general, the zoom in this game is heavily emphasized as a key control mechanic, and this is just one of the reasons why.