I'm currently having two issues that might be related.
I use Numix as theme and icons. And then, i have a secondary LCD monitor wich I use as primary and disable the one that is integrated with my laptop. And for having the LCD with a regular resolution I'd added one time long ago.
From nowhere, after one reboot i started to have this error (in short version)
Could not apply the stored configuration for monitors none of the selected modes were compatible with the possible modes:
With this, my custom resolution from the LCD monitor, dissapears, both monitors are mirrored, and theme design dissapears.
Googling a lot, I've found out that if a delete the monitors.xml inside ˜/.config the theme gets restore and if I reboot the machine, I don't get the error. BUT
When I'm going to change the monitor preferences as I want to, the monitors.xml gets created, and if i reboot, everything goes bananas again.
Some specs in case that helps
Ubuntu 16.04 Compaq CQ40-500la SamsungSyncMaster 943NWX