Is your checkbox in the Options page in HyperlinkTheme.xml
?
According to this answer from WiX developer Bob Arnson, all checkboxes except for the ones added to the Options page are simply ignored.
HyperlinkTheme.xml:
<Page Name="Options">
<Text X="11" Y="80" Width="-11" Height="30" FontId="2" DisablePrefix="yes">#(loc.OptionsHeader)</Text>
<Text X="11" Y="121" Width="-11" Height="17" FontId="3" DisablePrefix="yes">#(loc.OptionsLocationLabel)</Text>
<Editbox Name="FolderEditbox" X="11" Y="143" Width="-91" Height="21" TabStop="yes" FontId="3" FileSystemAutoComplete="yes" />
<Button Name="BrowseButton" X="-11" Y="142" Width="75" Height="23" TabStop="yes" FontId="3">#(loc.OptionsBrowseButton)</Button>
<Button Name="OptionsOkButton" X="-91" Y="-11" Width="75" Height="23" TabStop="yes" FontId="0">#(loc.OptionsOkButton)</Button>
<Button Name="OptionsCancelButton" X="-11" Y="-11" Width="75" Height="23" TabStop="yes" FontId="0">#(loc.OptionsCancelButton)</Button>
<!-- Additional checkbox control -->
<Checkbox Name="MyCheckBox" X="-11" Y="-173" Width="260" Height="17" TabStop="yes" FontId="3">#(loc.MyCheckbox)</Checkbox>
</Page>
If you did add it to the Options page, there might be a problem with the way to used the condition in the bundle.wxs
file. Try the method used in the question linked above and see how that works:
<Variable Name="MyVariable" Type="numeric" Value="![CDATA[MyCheckBox]]"/>