To All --
The other day after my initial post I did some additional research on this whole issue. As a result of some of this investigation, I'm not sure it's necessarily a "bug" per say with Fences, but, an issue with a Windows feature that is triggering this, and as a result Fences is restoring to what it believes was the original state of things, but the underlying setup of the monitors has been changed by Windows, and why the fences don't restore to the original state. However this might be a case where Fences can help resolve, or rather compensate for a Microsoft feature that probably could be turned off in some system configurations.
Windows is designed to auto detect the monitors when they are plugged in. You have probably noticed that when you either turn off 1 monitor in a 2 monitor config, windows detects the Monitor is no longer there, or available, so it re-configures the desktop and all the icons, etc that were on the disconnected monitor are moved to the remaining one. I believe this also happens when the monitors are set to "sleep" in the power settings of Windows, or even the settings on the monitor itself. Either way, when events happen where both monitors are set to sleep, or turn off themselves, or I turn them off, and then when the PC is brought out of sleep, or the monitors are turn on, the auto-detect feature kicks in, but since both of them are connecting on, or about the same time, I think the secondary monitor gets logged in first and therefore some of the settings are flipped in Windows (1 is now 2, and 2 is now 1) and this is where Fences is restored, it appears that it had flipped everything around. However, is the windows configuration of the monitors that really changed.
There are a lot of posts on the web asking if there is a way in Windows to disable that auto-detect. I don't think there is just a setting to be flipped, but there are some possible workarounds for this... maybe.. ? I don't want to give specific steps here because I believe the steps to work around this issue is going to be system specific, so what works for me might now work on others PCs and may make it worse even. But this might give some direction for your own investigation into options, and see where they can get Fences to possibly make a correction when this situation happens.
You could start by disabling Windows ability to put your monitors to sleep after a certain amount of time. That way, you've eliminated one scenario where this would happen. Look at the Windows Power Settings/Profiles, and look for the Monitor Sleep setting, and set to I believe it's "never".
Other people have suggested to modify Registry Keys (again, another reason I'm not going to give specific suggestions for a fix), and others have gone even farther to disable PINS on their HDMI cables to try to disable the auto detect - not all that successfully though. You might even find for sale adapters that you can plug in between the monitor and the HDMI cable that truly does disable this through the hardware, and no software changes are needed. I would guess that 2 off these devices, would correct the craziness you've been seeing in Fences all together as well.
Hope this helps a little... I will also try to post this in the ticket you created -- if I can access that, otherwise, maybe you might want to add this to your ticket as well, for the developers.
Regards,