Make sure you don't have any intermediate stops set in the Prescott area. You could also ask for a route between two points close to the 69/169 detour, maybe even the two intersections. There is, for a example a grade on that stretch of I17. Or maybe it has information (maybe old) on construction or blockage on that piece.
Regarding the Homer to Whittier route, it could be that it lacks information the tunnel drive to Whittier. My old copy of S&T sends me through Anchorate and Valdez. What does it recommend when you add a waypoint near Portage Glacier?
In the big picture, look at issues like shortest route v fastest route, tolls or not etc. But if a mapping program refuses to send me along a particular road, I play around with destinations close to that road, trying determine whether that road is in its database or not.