I have only flown the first three legs of the Alaska Bush Trip, but I had no problems switching the auto pilot to nav to follow the intended flight plan, even if the plan is not shown on the map. The CDI was set to GPS and displayed the CRS correctly.
This is not meant to say you are doing it wrong. Do you have any Garmin/AP mods installed? Asobo is doing something strange here to hide the flight plan from the map (VFR map and X-Cub Garmin display), so I imagine this could clash with mods.