There's a couple of possibilites come to mind
1. Naked Objects adds the route 'Ajax' so if you're adding any routes of your own with the name 'Ajax' it will fail with this error.
2. If you're not adding any routes of your own I wonder if RunMVC::RegisterGenericRoutes is being called twice for any reason. The obvious suspect is the change to the startup code now we've gone to using nuget. Is it possible that your startup code
is still calling RegisterRoutes in global.asax as well as NakedObjectsStart.cs ?
PS I'm not sure the route naming is very good. It should be more specific to avoid naming clashes if at all possible. I'll raise a ticket for this.