Please see this post for the solution.
Ok, I finally figured it out. The: AppDomain.CurrentDomain.GetAssemblies() piece of my code sometimes does not
For me this error had to do with where I put my CreateMap<>() call. I had put it in the static initializer for my DTO. When I moved the CreateMap<>() call to somewhere less cute, everything worked fine.
CreateMap<>()