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After you have your route all waypointed out if you click on the minimap and select route then current goto targets. It will optimize your route and "should not" ask you to cross over any way points.
From what I gather by your post you just imput the waypoints as you found them and didnt pay attention to the location on the continent. Carbonite dosen't know how to order the waypoints in favorites, i think. So far this is the only work around that I have found for it. Hope it helps
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