If you anticipate this rather unwanted behaviour, then one away around it would be to pass an extra parameter from the jQuery.trigger() to the checkbox's click handler. This extra parameter is to notify the click handler that click has been triggered programmatically, rather than by the user directly clicking on the checkbox itself. The checkbox's click handler can then invert the reported check status.
So here's how I'd trigger the click event on a checkbox with the ID "myCheckBox". Note that I'm also passing an object parameter with an single member, nonUI, which is set to true:
$("#myCheckbox").trigger('click', {nonUI : true})
And here's how I handle that in the checkbox's click event handler. The handler function checks for the presence of the nonUI object as its second parameter. (The first parameter is always the event itself.) If the parameter is present and set to true then I invert the reported .checked status. If no such parameter is passed in - which there won't be if the user simply clicked on the checkbox in the UI - then I report the actual .checked status:
$("#myCheckbox").click(function(e, parameters) {
var nonUI = false;
try {
nonUI = parameters.nonUI;
} catch (e) {}
var checked = nonUI ? !this.checked : this.checked;
alert('Checked = ' + checked);
});
JSFiddle version at http://jsfiddle.net/BrownieBoy/h5mDZ/
I've tested with Chrome, Firefox and IE 8.