The error was the exact same as in this post http://blogs.msdn.com/b/praburaj/archive/2013/12/02/owin-startup-class-not-detected.aspx
The solution was to totally empty the asp.net cache
Run this in PowerShell
net stop w3svc
Remove-Item -Path "C:\Windows\Microsoft.NET\Framework64\v4.0.30319\Temporary ASP.NET Files\root\*" -Force -Recurse
Remove-Item -Path "C:\Windows\Microsoft.NET\Framework\v4.0.30319\Temporary ASP.NET Files\root\*" -Force -Recurse
net start w3svc