I've got at work two external displays + a MBP 13" 2017. (OS: Mojave 10.14.1 Beta)
The monitors are both BenQ (GL2450), connected via HDMI to a Thunderbolt 3 port. (one through hub, one through plain adapter)
Now I have rotated the left screen by 90 degrees and set up the Internal Display on the right, it all works fine. Until I come back to work after disconnecting everything for > 1h. Then all my screens rotation are messed up, the normally pivoted display is back to default, and the default display is now rotated by 90 degrees, though I did NOT switch Ports on the MBP or Adapters.
Only way to fix this is to manoeuvre the mouse through messed up displays and go to the system settings and change everything back to normal. Problem there is, if I rotate the most left monitor (default -> 90), it asks for confirmation, and most of the times I can't reach it fast enough through the messed up displays. Interestingly enough, if I rotate the middle monitor first (90 -> default), it doesn't ask for permission.
It's annoying to do this every morning I arrive to work, though I started to see it as kind of a challenge. No the OS is not the problem ... I'm in this situation way longer than Mojave was announced.
EDIT: tried to narrow down the problem by plugging in cables at different times, rebooting, other monitors etc. nothing of that worked. I'm out of ideas.