[mapView setRegion:routeRegion animated:YES] scrolls/zooms the map to a different view to that when using animated:NO in the same function.
It looks like the centre point of the map is moved to the middle of the lower (southern) edge of the map with animate:YES is used. When animate:NO is used, the map is drawn as expected.
I've modified the Demo app in MacMapKit to illustrate this - download from: http://www.yellowfield.co.uk/macmapkit/MacMapKit-Animate_Issue.zip
On the main screen there's two additional buttons, one each for animate:YES and animate:NO. Clicking each button illustrates the problem.