I may have uncovered a bug in Setup Mode. If the Transport window is popped out, and I switch to Setup Mode and open the Clef and Transposition Overrides window for a layout, the Transport window stays on top (though its title bar color indicates that it is inactive) — even if I switch to another application like a web browser! I can’t close or even move the transport window until I close the C&TO dialogue first.
For comparison, I tried opening the transport bar and then Engraving Options, and didn’t have the same problem. I also tried opening Engraving Options and the C&TO window, and they behaved a little oddly with regard to what appeared on the taskbar and what was hidden when, but that’s a separate issue.
I’m using Windows 10 and Dorico 4.3.