ZDoom

Okay, thank you for testing that. Obviously this is an issue we'll have to look into, when we get the chance.

My main test case was Modern, but it seems like the Vintage build exhibits the same behavior. Upon further inspection, it seems that this behavior is only the case if the menu isn't open - if I alt-tab with the menu active, the mouse returns, and GZDoom no longer exclusively captures it if something outside of GZDoom is interacted with. My tendency is to open the console and tab out, though, and that's where the mouse-eating behavior happens (or if I tab while simply paused or so forth).

Which version is this? Modern or Vintage?

Can your system handle running the other version for test, to see if it happens there, too?

... if clicked while it is not the active window, i.e. you have alt-tabbed to some window that doesn't completely cover the screen and GZDoom is in the background. This only seems to affect exclusive fullscreen mode - windowed GZDoom does not capture your mouse like this. Having your mouse cursor eaten doesn't make GZDoom the active window, either, and the only way to get it back is completely closing GZDoom. I'm experiencing all of this on Windows 10, for reference.