The popups only identify the top-most layer that is being displayed. So even though your symbology for the boundaries (feature layers) may be hollow or transparent, these features are blocking your popups from identifying the dynamic layers. That's why they don't work when your feature layers are turned on. One way I've worked around this is to use the rsheitlin Identify Widget. You set which layers to identify and it will return all the results it encounters, not just the top-most.You can download it here: http://www.arcgis.com/home/item.html?id=39cf66d58c234279ba728c50461a1a89
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