CheckboxGroup (and RadioGroup, which extends it) collects it's children via:
var fields = this.panel.findBy(function(c){
    return c.isFormField;
}, this);
in onRender. This is problematic, because it collects any Ext form-type at any level. I was making a custom widget that contained an input box on the same line as a radio/checkbox, and noticing that everything was getting becoming 'false' when trying to set the value of the radios.

My quick fix was just to add "isFormField: false" to the configuration options of the non-radio widgets.