Starting with Xamarin 3.5, Xamarin.iOS automatically deploys the project whenever appropriate. Consequently, the "Deploy" checkboxes in the Configuration Manager are greyed-out. Unfortunately, they are displayed as un-checked, when in fact the default behavior is as if they were checked ON. See also:
We (the support team) have filed a bug to request that this "special" condition for Xamarin.iOS projects be changed slightly so that the checkboxes appear as always checked ON (instead of un-checked) to reduce confusion. Hopefully this change will appear in a release in the near future.