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Was there any conclusion to this issue as I am experiencing something broadly similar.
I am trying to create different portrait and landscape views on the iPad using the layered layout approach, ie one fixed layout pinned to top-left as the top layer, then beneath that a layout segment that slides to the right so that it displays in landscape orientation and beneath that a layout segment that slides to the bottom so that it displays in portrait mode.
The problem that I'm having is that any fields in a portal on one of the hidden segments actually appears above the other layout elements in FileMaker Go. In FileMaker Pro, the portal and its fields stay hidden, as you would expect.