The version I'm using is 2013, latest updates.
Phoenix to Flagstaff: Tried shortest and longest. No intermediate stops just Phoenix and Flagstyaff. Drag and drop doesn't help as it will still not route through I17. No problem with the 2008 version.
Homer to Whitter: Changed Homer to Portage and it still takes the marine ferry and then goes through the tunnel to Portage. Tried shortest and longest. I did try reset. An intermediate stop does cause it to use the Sterling Highway but should not be necessary IMHO. The 2008 version goes up the Sterling Highway as expected.
I'm beginning to think that both of these are program bugs and I saw other problems this summer. As I recall I could add intermediate stops to solve all of the problems except for the Phoenix to Flagstaff.
I was hoping someone else had 2013 and could confirm my results. Just like to know that it's not me.
BTW The program was still useful for planning and then tracking our route this summer.