Not exactly as you describe, perhaps; I experience something like that when window management goes awry; there's a dialog that has popped up somewhere and so the main window is unusable, but the dialog window is behind the main window, or off screen, or on another monitor behind a window hiding in the corner, etc. Sometimes I need to juggle things around to find it. I use "present windows" on KDE to show all the windows and sometimes that works, sometimes it doesn't. Maybe that's what's happening to you? This kind of thing happens on Windows too (not in reaper, IIRC) but it's more common on linux, unfortunately. Fortunately, it's a little easier to deal with on linux in some ways.
I believe with some window managers you can configure the task switcher to show each application vs each window (the latter showing dialog windows as their own options, rather than conflating.) Seem to remember windows has this as well.
With your hang, is there CPU usage?
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