I found the solution here: github.com/SignalR/SignalR/issues/3414
Snip sample:
public void Configuration(IAppBuilder app)
{
var task = Task.Run(() => app.MapSignalR());
task.Wait(300);
//try again if it fails just to be sure ;)
if (task.IsCanceled) Task.Run(() => app.MapSignalR()).Wait(300);
}