I've set my monitor's sleep at 10mins. so this issue happens quite frequently. I use sleep because sometimes I have to run off and see it a waste of power to leave monitors on.
I just installed the R9 390 Friday (today is sunday) I've been having this problem since I updated to 15.7.1, other than a hardware change thats the only difference.
I had a 280X before on 15.7 and never had these issues.
I have a 3 Monitors plugged into HDMI, DP and DVI ports of the R9 390.
I know, but I dont use eyefinity, the 3rd monitor is for presentations that I have preset so It disables my 2nd monitor and puts those visuals on the 3rd 46" TV.
Every time I wake from sleep, all windows on my 2nd monitor are shifted over to the disabled 3rd. so I have to pull them back every time.
2nd DVI to HDMI
3rd DP to HDMI
I would have used three DP to HDMI cables but I already had these cables before the AMD 280X, two are 15ft.