The checkboxes in the Salesforce Lightning Design System are odd ducks. They require a DOM structure that the Lightning component or aura ui:inputCheckbox tag doesn't support natively, due to the "slds-checkbox--faux" span, etc. Furthermore, the SLDS checkbox uses Ids to control the value between the faux span and the input:checkbox. I'm not sur…

1. Lightning Design System Checkbox Lightning Component (cmp)

<!-- LDS markup for a checkbox (https://www.lightningdesignsystem.com/components/forms/) -->
<div class="slds-form-element margintop10">
    <label class="slds-checkbox" for="requiredCheckbox">
        <ui:inputCheckbox aura:Id="requiredCheckbox" value="{!v.selectedFormObject.Required_On_Form__c}" />
        <span class="slds-checkbox--faux" />
        <span class="slds-form-element__label marginleft10">Required on Form?</span>
    </label>
</div>

2. Lightning Design System Checkbox Lightning Component Controller JS

({
    //Called from either another helper method or from the aura:initHandler call or an event, etc.
    doInit : function(component, event, helper) {
        return helper.fixLDSCheckboxes(component);
	}
})

3. Lightning Design System Checkbox Helper JS

({
    //Method for fixing Lightning Design System Checkboxes
    fixLDSCheckboxes : function(component){
        //Add all the checkboxes here.  Note, you'll need their aura Ids
        this.fixLDSCheckbox(component.find("requiredCheckbox"));
        this.fixLDSCheckbox(component.find("showLabelCheckbox"));
        this.fixLDSCheckbox(component.find("showCheckbox"));
        return false;
    },
    fixLDSCheckbox : function(chkbox){
    	var el = chkbox.getElement();
        var elLabel = el.parentElement;
        elLabel.setAttribute("for",el.getAttribute("Id"));
        return false;
	}
})