Update! So I finally found a way to make this work. I added a event to my controller to read the value of the checkbox and update the attribute. Not sure why I had to do this but it works. Would love to hear thoughts on why that is and whether or not I did the right thing. Either way I;m stoked to move on with this project. 

My New Code, cleaned up a few things as well: 

<aura:component access="global" implements="lightning:availableForFlowScreens">
    <aura:attribute name="proofSelection" type="String"/>
    <aura:attribute name="Changes" type="String"/>
    <aura:attribute name="Encoded_ID" type="String" />
    <aura:attribute name="DisclaimerValue" type="Boolean" default="false"/>
    <aura:attribute name="test" type="Boolean" default="false"/>
    <aura:attribute name="UploadFiles" type="Boolean" default="false"/>
	<aura:attribute name="radioOptions" type="List" default="[
      {'label': 'Yes', 'value': 'true'},
      {'label': 'No', 'value': 'false'} ]"/>

    <div style="width:400px;">
    <div class="slds-p-around_medium slds-p-bottom_medium" >
        
        <div class="slds-form slds-form_stacked">
			<lightning:select name="selectItem" label="How's the proof look?:" value="{!v.proofSelection}" class="slds-p-top_small"  >
        		<option value="-Select One-">-Select One-</option>
        		<option value="I approve my proof. Please proceed to print!">I approve my proof. Please proceed to print!</option>
        		<option value="I would like changes made to my proof.">I would like changes made to my proof.</option>
        	</lightning:select>           
            
    		<!-- If proof is not approved, also ask customer for changes. -->
        	<aura:if isTrue="{!v.proofSelection == 'I would like changes made to my proof.'}">
       			
					<div class="slds-form-element">
                	<lightning:textarea name="ChangesText" value="{!v.Changes}" label="Tell us what you'd like changed:" class="slds-p-top_small"/>
					<div class="slds-p-top_small"></div>
					<lightning:radioGroup aura:id="UploadFiles" name="UploadFiles"
                     label="Would you like to upload new content? (logos, images, etc)"
					options="{! v.radioOptions }" value="{! v.UploadFiles }" />
					<div class="slds-p-top_small"></div>
					</div>            
       		</aura:if>
            
        	<!-- If customer clicks yes to upload files show the file upload iframe. -->
            <aura:if isTrue="{! v.UploadFiles }" >      
            		<iframe src="{!'/TVA_CFB__RequestFile?'+v.Encoded_ID}" height="325px" width="325px" frameborder="0" class="slds-p-bottom_small"/>                                                                                                                             
            </aura:if>
          
        	<!-- If proof is  approved, askes customer for check box. -->
			<aura:if isTrue="{!v.proofSelection == 'I approve my proof. Please proceed to print!'}">
                       
        			<lightning:input aura:id="DisclaimerCheckBox" type="checkbox"
					label="I have proofread my artwork and am aware that Taradel is not responsible 
                    for any graphic, text, pricing, color variation or format issues after I submit 
                    the approval for print." 
                    name="DisclaimerCheckBox" value="DisclaimerCheckBox" onchange="{!c.handleCheck}" />
            </aura:if>  
          </div>
       <div class="slds-p-top_small"></div>    
       <lightning:button label="Finish and Save" aura:id="Finish_and_Save" 
       variant="neutral" onclick="{!c.handleChange}" />

        

    </div>
    </div>    
</aura:component>

My controller

({
   handleChange : function(component, event, helper) {
      // When an option is selected, navigate to the next screen
      var response = event.getSource().getLocalId();
      component.set("v.value", response);
      var navigate = component.get("v.navigateFlow");
      navigate("NEXT");
   },

    handleCheck : function(component, event, helper) {
        var isChecked = component.find("DisclaimerCheckBox").get("v.checked");
        component.set("v.DisclaimerValue", isChecked);
    }
 })