I second this as its really annoying in the maps. However my mouse doesn't line up with the thing I'm selecting so I'd be interested in knowing how you managed to get yours to work.
I think the mouse is working the same as it did in Horizons. If you click on a star, it selects the correct star.
But the little highlight circle and the "press to plot a route" annotations are still in the wrong place especially when they are near the edge of the screen.
At least the only thing you can do now is hold the select button to plot a route, you don't have to click on the annotation to create a bookmark etc. So it doesn't matter that the annotation is disconnected from the system. Except is looks a mess.