OWIN Web Api - responses suddenly return 404 on requests that recently returned 200

I've edited my question with some more relevant information.

I have a Owin Web-Api site that is hosted on IIS.

The application has a single controller with 2 actions.
The application works well. All actions return valid results.

When the application pool is recycled, the app starts returning 404's. Only rebuilding the bin directory (I'm currently working locally) will revive the application (stop\start on the application pool doesn't do anything positive).

This is how my Startup.cs looks like:

var httpConfiguration = new HttpConfiguration();
WebApiConfiguration.Register(httpConfiguration); // will show it's content later

appBuilder.UseRequestScopeContext(); // Third party OwinRequestScopeContext
appBuilder.Use<IOCContainerMiddleware>(); // Custom middleware that creates an IOC container per request and disposes it at the end of the request



name: "DefaultApi",
routeTemplate: "{controller}/{action}",
constraints: new { httpMethod = new HttpMethodConstraint(HttpMethod.Post) },
defaults: null);

ConfigureDependencyResolver(config); // Custom dependency resolver that uses the IOC container from above