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0e1f616
(Get the code!)
I just experienced this issue for the first time today.
I have an older monitor (Iiyama ProLite XB2380HS) and it is plugged into the lower DVI port on my Sapphire Radeon R9 380 Nitro.
I bought a new monitor (Iiyama G-Master GB2388HSU), and plugged it into the DisplayPort port on the same graphics card.
The former monitor is on the left, and the latter is on the right. I have four workspaces with two screens in each.
I wanted to get games to open up in the right hand monitor, so installed CCSM, and chose "Prefer smaller output" for Overlapping Output Handling.
This works fine, but when the screens suspend after a manual lock screen or automatically after 10 minutes, when I log back in, all of the applications in the left hand side of my workspaces have moved onto the right hand side.