On Sun, 18 Oct 2015, Graham Gillott wrote:

I don?t know how to fix this but I have had this problem on Yosemite also.
I have 4 monitors and this occasionally happens. I typically are using X11 apps 
through x2go on a remote host so if I quit and restart the session it comes 
back.
I had thought that this was something to do with the number of monitors I have 
especially since the 4th monitor is spanned over two smaller monitors using a 
matrox unit so I actually have 5 monitors attached. Clearly this is a core bug.
For any local apps I haven?t had this problem as much and in fact I can?t 
remember if I have however had problems with the local windows ?locking? and 
being un-resizable.

The apps I run are on a Debian machine. I have not run any X11 apps locally for ages, so I cannot really comment on that. Disabling "displays have separate spaces" fixes the problem; however, I've become very accustomed to having the menu bar on both displays since I frequently work on two documents at one time in (seperate) OS X-native apps. Ironically, I hated that feature when it was first introduced :)
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