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We have had some problems with popups on the a-layer, our developers are looking into it, the problem is intermittent, especially when using multiple popups. Most problems are solved by looking into how the plugin layers objects:
On the a-layers the plugin reads along the y-axis when exporting. The first object it "meets" will be arranged in the very front. The next object it "meets" will be arrange below the first object and so on.
So have a popup on the a-layer to be arranged in front of the other objects on the a-layer it has to be read first by the plugin, my suggestion is to group the popup with a transparent box that has the value y=0. And then having the rest of the a-layer below, meaning that they will have the y-value=0,001.
Then the popup should be arranged in front.
Let me know how it works out!