Gareth,
In the Filter\Widget.html make this edit (line 5 below):
data-dojo-props="checked:false"
<div class="custom-filter" data-dojo-attach-point="customFilterContainerNode">
<div class="title-part">
<span class="back-list" data-dojo-attach-event="click:_onBackToListClick"></span>
<span>${nls.customFilter}</span>
<div class="toggle-filter" data-dojo-type="jimu/dijit/ToggleButton" data-dojo-props="checked:false" title="${nls.toggleCustomFilters}" data-dojo-attach-event="change:_onCustomFilterToggle" data-dojo-attach-point="customFilterToggleButton"></div>
</div>