Comment 92 for bug 1292398

I have the same/similar issue with Ubuntu 15.10, Unity, NVidia GTX 970, NVidia-352 prop driver.

My main display (the left one) is 1920x1080 plugged in via HDMI, and my second monitor is 1280x1024 via DVI. I setup my big monitor to be the left one, and my smaller to be the right one via Unity display settings. On system boot, boot screen and information is only shown on my smaller right monitor, left monitor doesn't even get a signal. On login screen, login credentials are only shown on the smaller right screen, with an expanded wallpaper showing on the left.
After login, the left monitor is set correctly to the left, but full screen applications like most of my games start on the smaller right monitor by default. I can fix this after every login via NVidia Xserver Settings app and marking my left monitor as primary, then every game starts correctly on my left monitor. I worked around this now with a startup script setting the primary monitor to the left one via xrandr command.
Can't understand why this issue is still low, as it is a very annoying usability bug. Hope this get's fixed in 16.04 LTS!