Asp.net-mvc – OwinStartup not firing

I had the OwinStartup configuration code working perfectly and then it stopped working. Unfortunately I'm not sure exactly what I did to get it to stop working and am having a really hard time figuring it out.

To make sure I have the basics covered, I doubled checked to make sure the I have the

[assembly:OwinStartup(typeof(WebApplication.Startup))] 

attribute assigned properly and made sure that I don't have an appSetting for owin:AutomaticAppStartup that is set to false so I made one set to true to be safe as there was nothing there before.

<add key="owin:AutomaticAppStartup" value="true" />

I also tried specifically calling out the appSetting:

<add key="owin:appStartup" value="WebApplication.Startup" />

Before it stopped working I upgraded the Microsoft.Owin.Security NuGet packages to 2.0.2, so I tried reverting them to 2.0.1 (that was a pain) but it didn't change anything. I have WebActivator installed on the project and am using that to bootstrap other things but I've tested that on a fresh WebApplication template and it works there so I don't think that is the culprit.

I also tried removing my Startup class and using Visual Studio to add a new one using the OWIN Startup Class type in Add New Item and that isn't getting called either. Next I tried adding a second Startup class since I know it will throw an exception if there is more than one OwinStartup attributes defined, but it isn't throwing any exception there.

Not sure what else to try. Any thoughts?

Update

Turns out that Resharper removed the reference to Microsoft.Owin.Host.SystemWeb when I used it to remove unused references.