An update: I disabled synergy, set the monitor configuration to the
desired format and it worked.  Re-enabled synergy and all is happy now.
Have been through multiple reboot cycles and the monitor config is ok.

So for my case, this appears to be an interaction problem with synergy
and monitor configuration, with a fairly easy workaround.

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https://bugs.launchpad.net/bugs/1312342

Title:
  dual monitor breaks when not config'd for builtin monitor is to the
  left of second monitor

Status in “unity” package in Ubuntu:
  Confirmed

Bug description:
  Upgraded from 13.10 to 14.04 on my dual monitor system.  System
  consists of a system76 laptop (built in monitor is 1920x1080
  resolution) and an external monitor (ASUS 1920x1080 resolution).

  Prior to the upgrade, the monitors were configured with the ASUS
  monitor above the laptop monitor.  After the upgrade, the monitor
  configuration reverted to be configured with the laptop on the left
  (ASUS on the right).  When I use the Settings->Display tool to move
  the monitors to the previous configuration, it is no longer possible
  to move windows between the monitors or to move the cursor between the
  monitors.  This did work fine previously, so is a regression.  I have
  tried several other configurations, and none seem to work other than
  the default.

  One other note, I use synergy to provide keyboard and mouse from my
  desktop system (i.e., the laptop is the client).  This works fine, but
  since it does affect the mouse thought worth mentioning in case there
  was some interaction from that involved.

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