I've been bashing my head over this problem today. My Owin Startup class wasn't being executed. I'd followed the usual instructions of ensuring the "Microsoft.Owin.Host.SystemWeb" package was installed. I had the correct attribute on the assembly ([assembly: OwinStartup(typeof(StartupDemo.TestStartup))]), clearing the ASP.NET cache, etc etc.
Eventually I found that if you have set a friendly name for your startup class (in the instance where you may have multiple Startup.cs files) - then you need to also make sure you add the friendly name to your appSettings in the web.config too!
<add key="owin:appStartup" value="StartupDemo.ProductionStartup"/>
Doh!
