When I would deploy to the iOS simulator from Visual Studio I got a message that I hade to sync iOS SDK version with the build. But when I tried to sync I got an error that the sync process couldn't connect to the server.
Then I tried to open Xamarin Studio to check if there was any updates for any of the Xamarin products. And there was an update for Xamarin 3.1, after installing that update I could sync the iOS SDK without errors.
It looks like you have to install updates (other than the Visual Studio plugin) to Xamarin via Xamarin Studio.