Apologies for the late reply.
It sounds like the same problem to me, when I drop the cross hair onto the popup I get only the application beneath. Using Ctrl + Shift I cannot get the red border to appear on the popup or any other part of the application when the popup is up. When I dismiss
the popup Snoop works fine for the rest of the UI.
I am sure this is a limitation in my understanding of the visual tree and how Snoop works, I suspect the popup is somehow not in the structure which Snoop sees as the core application UI definition. I will add a sample application if there is more interest,
I debugged the UI for the popup the old school way so this is not blocking me.
Just wanted to add the Snoop is amazing - it's helped me so much.