Further to what I said above, I have tried a series of tests today with a colleague who is running a Nav V, (I have a VI) both of us with the latest software updates, and we went off route on a number of occasions missing Waypoints and Alerting Via points to see what happened. We both had auto-recalculation set to 'prompt' and 'auto skip wayoint' (only available on the Nav VI) set to 'off'. All other navigation settings were set to 'off' or manual - no avoidances. Fastest route set.
If we went off-route, and said 'no' to the recalculation prompt, it would asume that we would get back on route at the point where we left off, and it would not be happy until we did - assuming that there was a waypoint ot alerting point that we missed or by-passed nearby. Manually skipping that waypoint (which we had already passed) set us back on course again to the destination along the planned route once the route was rejoined.
Just to confirm, both our Navs were set to 'do not recalculate', and it wouldn't when we made a detour. The purple route stayed fixed where it was. If we allowed it to recalculate, it would try to get us back on the planned route again at the nearest point.
When we went back to test the same route, but this time saying 'yes' to the recalculation prompt, at exactly the same point where we strayed off route before, it would try to recalculate us back on route, back through the nearest waypoint that we missed. If there were no waypoints that we missed on the detour, it would take us the fastest route back to the planned route before the next waypoint.
Having 'auto-skip waypoint' ticked would mean that it used a little intelligence (always dangerous with a box of electronics) and just routed us to the nearest next waypoint in front of us to get us back on route.
Basically, I was not seeing any of the problems mentioned above of the Nav recalculating its own merry route to the destination. Everytime, it tried to get us back on track at some stage.
I assume that it must be the settings on the Nav itself that is causing the issue, or else we would have replicated what you are seeing? Mind you, it was a very short route that we tested due to time constraints, so that needs to be borne in mind.
We were testing this as we are off to Spain soon and want to get this right and understand how the Nav behaves when things dont go as planned.