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In Alteryx Designer x64 10.6.6.17413 running Windows 7 Enterprise, running Maximized full screen on a multi-screen display:
When I add a new Input Data connection, and the "Choose Table or Specify Query" window pops, it actually appears behind the main "canvas" window. Because it is modal, you can't click anywhere on the main window, it does not appear in the task bar, but instead you have to Alt-Tab to find the popup to select it.
If the window is not full-screen, then the modal window pops up in front of the canvas correctly.
I experience a version of this issue still in 2019.1, on a Windows 7 machine. When I click on Table or Query, the modal window pops up correctly, BUT if I click away from Alteryx, the modal window disappears and the only way I can get it back is to minimize all my programs, go to the desktop, then click on the Alteryx icon in the task bar. It's confusing if I've forgotten that I'd opened it because the main Alteryx window is completely unresponsive until I can get the pop-up back and close it.