A code sample says 1000 words:

    <input type="checkbox" onclick="alert(this.checked?'yes':'no')" id="test" />

Pretty simply unchecked checkbox. Clicking on it will check it and then alert "Yes"

However, doing the same thing with jQuery:

    $('#test').click()

Excutes in the opposite it order. It will alert "No", and then check the checkbox.

Suspect the FIRST action should be to change the checked status, followed by onclick() and other Click events.