Hi, I have also had this problem since 10.11.  No sleep required, just
locking the screen can create the behavior.  I can also reproduce.
There is a fix however, at least for me.

The problem occurs when I invoke xterm with geometry, however if I use
xterm and then move the window it will not occur even though the end
state geometry is identical.

e.g.:

xterm -geometry 121x103+1708+0 # lock screen, its hidden or moved
after logging back in.

IIRC from my testing it may be the +0 y coord as part of the problem
or that the right edge is beyond or on max X.

If I do this:

xterm -geometry 121x103 &
PID=$!
sleep 1
WID=$(xdotool search --all --pid $PID 2>/dev/null)
xdotool windowmove --sync $WID 1708 0 2>/dev/null
xdotool windowmove --sync $WID 1708 0 2>/dev/null

Then it does not move or hide automatically after lock screen or
sleep.  And yes, for some reason I have to call xdotool twice when
moving the window (I cannot recall why).

Manual move with mouse also appears to fix the mystery problem.

Facts: OSX 10.11.6, Xquartz 2.7.9, 15" MBP 2016, 27" apple display,
MBP lid closed, only using external display.  Also using multiple
virtual desktops.

Cheers,

Egan

On Tue, Oct 4, 2016 at 9:52 AM, William Ray Wing <[email protected]> wrote:
>
>> On Oct 4, 2016, at 11:26 AM, Michael Jinks <[email protected]> wrote:
>>
>> On Mon, Sep 26, 2016 at 8:23 AM, Tom Lane <[email protected]> wrote:
>>>
>>> BTW, I was mildly astonished to find out that this problem seems gone
>>> after updating to Sierra.  There might be corner cases where it's still
>>> problematic, but at least for my use-cases it's enormously better.
>>> (Still on XQuartz 2.7.9 btw.)
>>
>> Well, crumbs: I knew this day would come, but drat anyway, sez here my
>> MacBook Pro was born "Mid 2009", and it sez over there that Sierra
>> only goes back to 2010.
>>
>
> You might want to take a look here:
>
> http://forums.macrumors.com/threads/macos-10-12-sierra-unsupported-macs-thread.1977128/
>
> Where a patching application and script are allowing folks to install Sierra 
> (very successfully) on quite a number of Macs that Apple has chosen to stop 
> supporting.  Speculation is that in at least some cases, the drop is because 
> some models didn’t sell well enough to make it worth Apple’s time and 
> resources to vet all possible configurations with all possible combinations 
> of installed software in their testing lab.
>
> -Bill
>
>
>
>> So, if anybody has insight that might brighten my day... Otherwise,
>> been shopping for Linux-happy laptops already so maybe that project
>> just picked up some speed, if Apple no longer supports the hardware
>> I'm on currently.
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