I’ve been having similar if not same problem. It doesn’t happen consistently. I’ve removed the platform ios and reinstalled it.
This is my setup:
Cordova CLI: 6.4.0
Ionic CLI Version: 2.1.18
Ionic App Lib Version: 2.1.9
ios-deploy version: 1.9.0
ios-sim version: 5.0.13
OS: OS X El Capitan
Node Version: v6.9.2
Xcode version: Xcode 8.2 Build version 8C38
I have found that toggling the keyboard seems to help with text fields (Cmd-K). But I haven’t found a solution for the checkboxes when focus is lost.