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Recently, I'm observing weird behavior when switching between applications and also when switching between some Finder windows. I'm using an external 4K monitor with my MacBook Pro Retina. It is as if I have two displays fighting to be shown on the 4K monitor, with my windows split between the two, some on one, some on the other. When I use Alt-Tab to switch between applications, half are in one display and the rest in another display, such that when switching to one in a different half the screen as a whole shifts left or shifts right by a full screen width to reveal the display that are in the current set, as if the two displays were to the left and right of each other. When in the Finder, using Ctrl-Tab to switch between windows only half are cycled through, with an extra blank position in the cycle with no window receiving focus. If I manually choose Window menu to select window that was not in the current cycle, I end up in the other set, and can cycle through those now.

I'm not sure whether this is a feature or a bug. I haven't tried rebooting yet, due to the loss of state a reboot causes in my setup that I would like to avoid and have no guarantee that a reboot would fix this.

Strangely, the desktop shows the same icons for files in the two displays, however, the desktop background differs. In one half it is solid blue, in the other, it is the El Capitan default image provided by Apple.

Forcing the Finder to relaunch did not resolve the issue.

How can I get all my applications and windows back together on a single display so all are visible at the same time? Is this a bug or a feature?

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    Are you sure it's not mission control/spaces? Swipe up with 3 fingers to see all your Spaces. – At0mic Jul 8 '16 at 0:39
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    It's probably Spaces, combined with "Displays have separate Spaces" - System Prefs > Mission Control & also trying to use one app with windows on different Spaces, which is why they will not restore after reboot as you anticipate. See support.apple.com/kb/PH21872?locale=en_US – Tetsujin Jul 8 '16 at 7:33

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