I can confirm the same problem exists with Xubuntu x64 16.04 as well.
However I can also confirm that this has been a problem with all Ubuntu
flavors for many years.
The difference now is that nothing can be done on the user side to fix
it. After all these years I'd become quite adept at editing display.xml
and monitor.xml files, xorg.conf files, etc. but now none of that works.
The only thing I haven't tried is changing Compiz settings, but that's
because Xubuntu doesn't run Compiz by default, and people running Compiz
have already reported that it can't be fixed their anyway.
I know the developers work hard and always have their plates full, but
if they could at least fix it enough that we could edit conf files again
it would be great.
** Also affects: xfwm4 (Ubuntu)
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Cannot set right monitor as primary in dual monitor configuration
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