If you visit the flipswitch demo here, http://demos.jquerymobile.com/1.4.5/flipswitch, you'll see this code used for custom labels:
<form>
<label for="flip-checkbox-3">Flip toggle switch checkbox:</label>
<input type="checkbox" data-role="flipswitch" name="flip-checkbox-3" id="flip-checkbox-3" data-on-text="Assured" data-off-text="Uncertain" data-wrapper-class="custom-size-flipswitch">
</form>
However, what isn't made clear is that you are supposed to specify CSS to make the labels fit. This is documented over on the API docs area, but it is entirely possible a person will just use the demo code and assume it will work.