TL;DR - if the windows are moving to a VGA connected monitor, it looks like there are three options, in order of "fixed" to "workaround":
* Change the connection to that monitor to something other that VGA (changing to DisplayPort connection fixed it for me)
* Make the VGA monitor the Primary Monitor.
* Unplug the VGA monitor, then plug it back on each resume.
I had this problem - all the windows shifted to one monitor on resume from sleep / hibernate. The LCD monitor the windows shifted to was connected by VGA cable - my primary monitor is connected by DisplayPort, plus the laptop display.
Turning off the VGA monitor didn't force the windows to shift back to the primary monitor, but unplugging the VGA monitor did force the windows back.
I guess that the VGA connection does not report that the monitor is actually off, just that there is a monitor present, and Windows detects it before the DisplayPort connected monitor or even the internal laptop display, so moves the Windows to the VGA monitor.
Fortunately, the VGA connected monitor also has DisplayPort connection, so I changed the monitor to DisplayPort, and the problem was resolved.