How do you check a checkbox without firing a change event?

You should suspend events before set the value and resume events after this. For example:

myCheckBox.suspendEvents(false); // Stop all events. 
                                 //Be careful with it. Dont forget resume events!
myCheckBox.setValue(!myCheckBox.getValue()); // invert value
myCheckBox.resumeEvents(); // resume events

Why dont you just set

r.checked = true, 

does that not work? although it should work.

Why dont you just set r.checked = true, does that not work?

Setting checked attributes will have affect only for non-rendered control to assign initial control value. After rendering you can't use this to change value.

Suspend/Resume events is good practice to change control value without sending notifications.

Also you can put checked state immedially to dom element:

item.el.dom.checked = true;