ASP.NET does heavily cache all the providers. I am caching the config but the runtime is caching the actual provider collection. Sometimes just rebuilding with VS doesn't clear the cache but if you make a small change in Web.config it should clear it, or restart IIS if all else fails. My guess is yours was still cached without the FakeIndexBuilder provider (which is new). All the specific IndexBuilderProviders inherit from IndexBuilderProvider so the IndexBuilderManager only deals with them as the base class.
Are you still getting this error after restarting IIS?
Thanks,
Joe