It appears that most of the routes in your example include a VOR entry/exit point that shares the same ID as a nearby NDB (e.g. GV, CS, AS, AYE). This is causing the problem, because the application will sometimes default to the NDB if it is nearer to the direct route. However, since the NDB is not the entry/exit point to the airway, the route fails.
Strange.. the FMS I use insists on NB following a navaid name.. e.g. Richmond NDB is RICNB ...
I thought our FMS was using Jeppesen NavData.. wonder why there software would be different?