AngularJS Checkbox not working

You are trying to force too complex solution. To start with, you do not need ng-checked nor ng-change when you are using ng-model.

Let's say you have the following controller

app.controller('MainCtrl', function($scope) {
  $scope.case = { 
    caseId: 0,
    steps: [
      { id: 1, name: 'First step', enabled: true }, 
      { id: 2, name: 'Second step', enabled: false },
      { id: 2, name: 'Third step', enabled: false }]
    };
});

And related HTML

<div ng-repeat="step in case.steps">
  <input type="checkbox" ng-model="step.enabled">&nbsp;{{ step.name }}
</div>

That's all it takes!

Example Plunk here http://plnkr.co/edit/QjD91l

Edit:

If you need to do some processing based on selection, then yes, you could add ng-change to input control. Then HTML becomes

<input type="checkbox" ng-model="step.enabled" ng-change="stateChanged(step)">&nbsp;{{ step.name }}

And in controller

$scope.stateChanged = function(step){
  console.log('Changed step id:' + step.id + ' enabled state to ' + step.enabled;   
};  

I had to abandon ng-model for my checkbox as it was not picking up the initial value that was set in the model (in response to a service call). All of the other input controls were responding correctly to the model (and, interestingly, were correctly enabled/disabled based on the value backing the checkbox).

Instead, I used the 'checked' attibute and ng-click, as so:

<input type="text" ng-disabled="!myModel.isFruit" ng-model="myModel.seedCount">

<input type="checkbox" checked="{{myModel.isFruit}}" ng-click="onFruitClicked()"> Is Fruit

In my controller:

$scope.myModel = {
    isFruit : myServices.getIsFruit(),
    seedCount : myServices.getSeedCount()
};

$scope.onFruitClicked = function() {
    // toggle the value
    $scope.myModel.isFruit = !$scope.myModel.isFruit;
    // save the new value
    myServices.setIsFruit($scope.myModel.isFruit);
};