Maybe same issue as https://github.com/doitsujin/dxvk/issues/3269
I don't expect this to do anything but does it help if you launch with d3d9.enableDialogMode = True ?
d3d9.enableDialogMode = True
This has already been tried and no effect is seen.
This problem had been gone for a while after 2.0, but it came back when the nvidia driver was updated, so I believe that the nvidia driver update probably had some effect on the problem.
In any case, this did not happen with dgVoodoo or native direct X.
When full-screen window mode are enabled, the display priority order for sub-windows is not working properly.

A particular scene in this game consists of a main 3D view and a sub-window, as shown in the image below.
Originally, the subwindow (In the image, the one in the upper right corner of the screen) would remain visible when the main 3D view is clicked, but with DXVK, the subwindow disappears when the main 3D view is clicked.
Software information
Artificial Academy 2 (with AA Unlimited)
System information
Apitrace file(s)
https://drive.google.com/file/d/1aIgi_sFUIkpen--B2RyNq996hSPuTUtZ/view?usp=sharing
Log files